Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/inputs/xbh Working: n-5-32.cluster.ucsf.bkslab.org:/scratch/xiaobo/182395/xbh-8058088.34 Result: /scratch/xiaobo/182395/xbh-8058088.34 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbh 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/xbh mkdir: created directory `/scratch/xiaobo/182395' mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34' /scratch/xiaobo/182395/xbh-8058088.34 /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/182395/xbh-8058088.34/working' mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/protonate' Storing results in /scratch/xiaobo/182395/xbh-8058088.34/finished Working in /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 /scratch/xiaobo/182395/xbh-8058088.34/working/protonate /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Using inputs as protomers/tautomers. No processing done 481 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/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Bulk generating 3D conformations all protomers in /scratch/xiaobo/182395/xbh-8058088.34/working/3D mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/182395/xbh-8058088.34/working/protonate/xbh-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 ZINC001357240732 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building' mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357240732' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357240732 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001357240732 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357240732/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357240732 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/1 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](Cc1ccc(Cl)cc1)c1ccccc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001357240732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357240732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357240732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357240732 none O=C(N[C@@H](Cc1ccc(Cl)cc1)c1ccccc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.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.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 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] 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] 0 hydrogens 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, 7, 7, 21, 23, 23, 21, 23, 23, 23, 7, 10, 10, 7, 10, 10, 1, 1, 1, 8, 8, 8, 8, 9, 9, 8, 9, 9, 8, 4, 21, 21, 23, 23, 23, 23, 10, 10, 7, 10, 10, 8, 9, 9, 8, 9, 9, 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, 50]) total number of confs: 129 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357240732 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357240732 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/finished' Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357240732/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357240732 Building ZINC001357273639 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357273639 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/2 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C(F)(F)F)c1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001357273639.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357273639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001357273639 none O=C(Nc1cccc(C(F)(F)F)c1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens 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, 10, 14, 14, 46, 46, 14, 46, 46, 46, 46, 46, 46, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 46, 46, 18, 46, 10, 10, 10, 10, 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]) total number of confs: 153 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/3 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/3' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C(F)(F)F)c1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001357273639.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357273639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001357273639 none O=C(Nc1cccc(C(F)(F)F)c1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens 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, 10, 15, 17, 49, 50, 44, 50, 50, 50, 50, 48, 49, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 17, 48, 50, 48, 48, 10, 10, 10, 10, 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]) total number of confs: 134 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357273639 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639 Building ZINC001357273639 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357273639 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 2) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(C(F)(F)F)c1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001357273639.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357273639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001357273639 none O=C(Nc1cccc(C(F)(F)F)c1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens 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, 10, 14, 14, 46, 46, 14, 46, 46, 46, 46, 46, 46, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 46, 46, 18, 46, 10, 10, 10, 10, 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]) total number of confs: 153 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 3) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(C(F)(F)F)c1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001357273639.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357273639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001357273639 none O=C(Nc1cccc(C(F)(F)F)c1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens 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, 10, 15, 17, 49, 50, 44, 50, 50, 50, 50, 48, 49, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 17, 48, 50, 48, 48, 10, 10, 10, 10, 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]) total number of confs: 134 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357273639 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357273639 Building ZINC001357289998 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357289998 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/4 `/scratch/xiaobo/182395/xbh-8058088.34/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)Nc1c(C)cc(Br)cc1C) `ZINC001357289998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357289998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001357289998 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(C)cc(Br)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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.3', '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', '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, 5, 1, 1, 17, 1, 1, 5, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 6, 10, 10, 4, 4, 1, 1, 1, 1, 8, 8, 8, 13, 13, 13, 8, 10, 13, 13, 13, 4, 4, 4, 10, 10, 7, 10, 10, 4, 4, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13] 21 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 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: 64 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/5 `/scratch/xiaobo/182395/xbh-8058088.34/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)Nc1c(C)cc(Br)cc1C) `ZINC001357289998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357289998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001357289998 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(C)cc(Br)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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.3', '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', '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, 5, 1, 1, 17, 1, 1, 5, 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 14, 14, 5, 14, 14, 5, 5, 1, 1, 1, 1, 8, 8, 8, 13, 13, 13, 8, 8, 13, 13, 13, 5, 5, 5, 14, 14, 5, 14, 14, 5, 5, 5, 8, 13, 13, 13, 13, 13, 13, 13, 13] 28 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 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: 74 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357289998 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998 Building ZINC001357289998 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357289998 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 4) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)Nc1c(C)cc(Br)cc1C) `ZINC001357289998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357289998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001357289998 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(C)cc(Br)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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.3', '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', '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, 5, 1, 1, 17, 1, 1, 5, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 6, 10, 10, 4, 4, 1, 1, 1, 1, 8, 8, 8, 13, 13, 13, 8, 10, 13, 13, 13, 4, 4, 4, 10, 10, 7, 10, 10, 4, 4, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13] 21 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 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: 64 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 5) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)Nc1c(C)cc(Br)cc1C) `ZINC001357289998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357289998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001357289998 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(C)cc(Br)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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.3', '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', '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, 5, 1, 1, 17, 1, 1, 5, 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 14, 14, 5, 14, 14, 5, 5, 1, 1, 1, 1, 8, 8, 8, 13, 13, 13, 8, 8, 13, 13, 13, 5, 5, 5, 14, 14, 5, 14, 14, 5, 5, 5, 8, 13, 13, 13, 13, 13, 13, 13, 13] 28 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 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: 74 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357289998 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357289998 Building ZINC001357347110 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357347110 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/6 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1ccccc1)c1ccc2nc(C(F)(F)F)[nH]c2c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001357347110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357347110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001357347110 none O=C(N[C@@H](c1ccccc1)c1ccc2nc(C(F)(F)F)[nH]c2c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 6, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 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, 7, 4, 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] 0 hydrogens 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, 8, 8, 18, 18, 14, 18, 18, 8, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 18, 18, 16, 18, 18, 44, 44, 44, 3, 3, 3, 3] 50 rigid atoms, others: [1, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 114 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/7 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/7' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1ccccc1)c1ccc2nc(C(F)(F)F)[nH]c2c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001357347110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357347110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001357347110 none O=C(N[C@@H](c1ccccc1)c1ccc2nc(C(F)(F)F)[nH]c2c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 6, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 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, 7, 4, 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] 0 hydrogens 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, 9, 9, 18, 18, 10, 18, 18, 9, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 18, 18, 10, 18, 18, 45, 45, 45, 3, 3, 3, 3] 50 rigid atoms, others: [1, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 119 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357347110 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110 Building ZINC001357347110 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357347110 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 6) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](c1ccccc1)c1ccc2nc(C(F)(F)F)[nH]c2c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001357347110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357347110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001357347110 none O=C(N[C@@H](c1ccccc1)c1ccc2nc(C(F)(F)F)[nH]c2c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 6, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 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, 7, 4, 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] 0 hydrogens 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, 8, 8, 18, 18, 14, 18, 18, 8, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 18, 18, 16, 18, 18, 44, 44, 44, 3, 3, 3, 3] 50 rigid atoms, others: [1, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 114 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 7) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](c1ccccc1)c1ccc2nc(C(F)(F)F)[nH]c2c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001357347110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357347110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001357347110 none O=C(N[C@@H](c1ccccc1)c1ccc2nc(C(F)(F)F)[nH]c2c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 6, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 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, 7, 4, 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] 0 hydrogens 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, 9, 9, 18, 18, 10, 18, 18, 9, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 18, 18, 10, 18, 18, 45, 45, 45, 3, 3, 3, 3] 50 rigid atoms, others: [1, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 119 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357347110 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347110 Building ZINC001357347118 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357347118 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/8 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1ccccc1)c1ccc2nc(C(F)(F)F)[nH]c2c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001357347118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357347118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001357347118 none O=C(N[C@H](c1ccccc1)c1ccc2nc(C(F)(F)F)[nH]c2c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 6, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 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, 7, 4, 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] 0 hydrogens 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, 8, 8, 17, 17, 10, 17, 17, 8, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 8, 17, 17, 44, 44, 44, 3, 3, 3, 3] 50 rigid atoms, others: [1, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 116 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/9 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/9' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1ccccc1)c1ccc2nc(C(F)(F)F)[nH]c2c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001357347118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357347118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001357347118 none O=C(N[C@H](c1ccccc1)c1ccc2nc(C(F)(F)F)[nH]c2c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 6, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 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, 7, 4, 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] 0 hydrogens 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, 8, 8, 18, 18, 10, 18, 18, 8, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 18, 18, 10, 18, 18, 44, 44, 44, 3, 3, 3, 3] 50 rigid atoms, others: [1, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 116 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357347118 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118 Building ZINC001357347118 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357347118 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 8) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(N[C@H](c1ccccc1)c1ccc2nc(C(F)(F)F)[nH]c2c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001357347118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357347118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001357347118 none O=C(N[C@H](c1ccccc1)c1ccc2nc(C(F)(F)F)[nH]c2c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 6, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 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, 7, 4, 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] 0 hydrogens 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, 8, 8, 17, 17, 10, 17, 17, 8, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 8, 17, 17, 44, 44, 44, 3, 3, 3, 3] 50 rigid atoms, others: [1, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 116 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 9) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(N[C@H](c1ccccc1)c1ccc2nc(C(F)(F)F)[nH]c2c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001357347118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357347118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001357347118 none O=C(N[C@H](c1ccccc1)c1ccc2nc(C(F)(F)F)[nH]c2c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 6, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 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, 7, 4, 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] 0 hydrogens 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, 8, 8, 18, 18, 10, 18, 18, 8, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 18, 18, 10, 18, 18, 44, 44, 44, 3, 3, 3, 3] 50 rigid atoms, others: [1, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 116 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357347118 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357347118 Building ZINC001357363112 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357363112 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/10 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Cl)cc2)CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357363112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357363112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357363112 none O=C(NCC1(c2ccc(Cl)cc2)CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 8, 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: [4, 1, 4, 4, 23, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 7, 7, 7, 7, 7, 4, 14, 14, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 7, 7] 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: 115 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/11 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/11' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Cl)cc2)CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357363112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357363112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357363112 none O=C(NCC1(c2ccc(Cl)cc2)CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 8, 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, 20, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 7, 7, 7, 7, 7, 3, 14, 14, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7, 7] 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: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357363112 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112 Building ZINC001357363112 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357363112 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 10) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCC1(c2ccc(Cl)cc2)CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357363112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357363112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357363112 none O=C(NCC1(c2ccc(Cl)cc2)CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 8, 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: [4, 1, 4, 4, 23, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 7, 7, 7, 7, 7, 4, 14, 14, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 7, 7] 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: 115 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 11) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCC1(c2ccc(Cl)cc2)CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357363112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357363112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357363112 none O=C(NCC1(c2ccc(Cl)cc2)CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 8, 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, 20, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 7, 7, 7, 7, 7, 3, 14, 14, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7, 7] 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: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357363112 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357363112 Building ZINC001357370780 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357370780 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/12 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)cc1)[C@@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001357370780.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357370780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001357370780 none O=C(Nc1ccc(F)cc1)[C@@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', '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', 'C.2', 'C.2', 'Cl', 'S.3', '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, 15, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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, 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] 0 hydrogens 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, 6, 20, 20, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 2, 5, 1, 1, 1, 8, 8, 8, 8, 8, 20, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8] 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/13 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/13' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)cc1)[C@@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001357370780.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357370780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001357370780 none O=C(Nc1ccc(F)cc1)[C@@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', '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', 'C.2', 'C.2', 'Cl', 'S.3', '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, 15, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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, 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] 0 hydrogens 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, 12, 28, 28, 33, 33, 28, 29, 33, 33, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 12, 1, 1, 1, 9, 9, 9, 9, 9, 28, 33, 33, 33, 33, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9] 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357370780 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780 Building ZINC001357370780 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357370780 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 12) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(Nc1ccc(F)cc1)[C@@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001357370780.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357370780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001357370780 none O=C(Nc1ccc(F)cc1)[C@@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', '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', 'C.2', 'C.2', 'Cl', 'S.3', '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, 15, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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, 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] 0 hydrogens 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, 6, 20, 20, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 2, 5, 1, 1, 1, 8, 8, 8, 8, 8, 20, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8] 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 13) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(Nc1ccc(F)cc1)[C@@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001357370780.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357370780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001357370780 none O=C(Nc1ccc(F)cc1)[C@@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', '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', 'C.2', 'C.2', 'Cl', 'S.3', '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, 15, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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, 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] 0 hydrogens 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, 12, 28, 28, 33, 33, 28, 29, 33, 33, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 12, 1, 1, 1, 9, 9, 9, 9, 9, 28, 33, 33, 33, 33, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9] 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357370780 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370780 Building ZINC001357370781 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357370781 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/14 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)cc1)[C@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001357370781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357370781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001357370781 none O=C(Nc1ccc(F)cc1)[C@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', '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', 'C.2', 'C.2', 'Cl', 'S.3', '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, 15, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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, 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] 0 hydrogens 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, 24, 24, 33, 33, 24, 27, 33, 33, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 2, 10, 1, 1, 1, 9, 9, 9, 9, 9, 24, 33, 33, 33, 33, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9] 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/15 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/15' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)cc1)[C@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001357370781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357370781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001357370781 none O=C(Nc1ccc(F)cc1)[C@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', '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', 'C.2', 'C.2', 'Cl', 'S.3', '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, 15, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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, 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] 0 hydrogens 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, 11, 22, 22, 32, 32, 22, 27, 32, 32, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 2, 10, 1, 1, 1, 10, 10, 10, 10, 10, 22, 32, 32, 32, 32, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357370781 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781 Building ZINC001357370781 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357370781 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 14) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1ccc(F)cc1)[C@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001357370781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357370781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001357370781 none O=C(Nc1ccc(F)cc1)[C@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', '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', 'C.2', 'C.2', 'Cl', 'S.3', '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, 15, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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, 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] 0 hydrogens 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, 24, 24, 33, 33, 24, 27, 33, 33, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 2, 10, 1, 1, 1, 9, 9, 9, 9, 9, 24, 33, 33, 33, 33, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9] 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 15) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1ccc(F)cc1)[C@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001357370781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357370781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001357370781 none O=C(Nc1ccc(F)cc1)[C@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', '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', 'C.2', 'C.2', 'Cl', 'S.3', '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, 15, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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, 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] 0 hydrogens 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, 11, 22, 22, 32, 32, 22, 27, 32, 32, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 2, 10, 1, 1, 1, 10, 10, 10, 10, 10, 22, 32, 32, 32, 32, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357370781 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357370781 Building ZINC001357379374 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357379374 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/16 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/16' -> `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)NCCc1ccccc1Cl) `ZINC001357379374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357379374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001357379374 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', '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'] dock atom type 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, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 8, 8, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/17 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/17' -> `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)NCCc1ccccc1Cl) `ZINC001357379374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357379374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001357379374 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', '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'] dock atom type 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, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 12, 13, 13, 12, 13, 13, 13, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 9, 9, 12, 12, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357379374 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374 Building ZINC001357379374 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357379374 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 16) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1ccccc1Cl) `ZINC001357379374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357379374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001357379374 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', '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'] dock atom type 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, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 8, 8, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 17) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1ccccc1Cl) `ZINC001357379374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357379374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001357379374 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', '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'] dock atom type 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, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 12, 13, 13, 12, 13, 13, 13, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 9, 9, 12, 12, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357379374 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357379374 Building ZINC001357380689 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357380689 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/18 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1NC(=O)[C@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001357380689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357380689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357380689 none Cc1ccccc1NC(=O)[C@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', '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', '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, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 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, 4, 7, 6, 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] 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: [32, 32, 32, 24, 32, 32, 24, 24, 10, 24, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 2, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 24, 32, 32, 24, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4] 33 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/19 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/19' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1NC(=O)[C@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001357380689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357380689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357380689 none Cc1ccccc1NC(=O)[C@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', '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', '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, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 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, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 22, 34, 34, 22, 22, 9, 22, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 2, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 34, 34, 34, 34, 22, 34, 34, 22, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5] 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: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357380689 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689 Building ZINC001357380689 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357380689 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 18) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccccc1NC(=O)[C@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001357380689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357380689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357380689 none Cc1ccccc1NC(=O)[C@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', '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', '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, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 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, 4, 7, 6, 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] 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: [32, 32, 32, 24, 32, 32, 24, 24, 10, 24, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 2, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 24, 32, 32, 24, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4] 33 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 19) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccccc1NC(=O)[C@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001357380689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357380689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357380689 none Cc1ccccc1NC(=O)[C@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', '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', '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, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 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, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 22, 34, 34, 22, 22, 9, 22, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 2, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 34, 34, 34, 34, 22, 34, 34, 22, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5] 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: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357380689 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380689 Building ZINC001357380690 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357380690 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/20 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1NC(=O)[C@@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001357380690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357380690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357380690 none Cc1ccccc1NC(=O)[C@@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', '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', '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, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 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, 4, 7, 6, 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] 0 hydrogens 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, 19, 35, 35, 19, 19, 5, 19, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 22, 35, 35, 19, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4] 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: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/21 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/21' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1NC(=O)[C@@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001357380690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357380690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357380690 none Cc1ccccc1NC(=O)[C@@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', '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', '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, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 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, 4, 7, 6, 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] 0 hydrogens 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, 24, 37, 37, 24, 24, 9, 24, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 37, 37, 37, 37, 25, 37, 37, 24, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5] 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: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357380690 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690 Building ZINC001357380690 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357380690 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 20) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccccc1NC(=O)[C@@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001357380690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357380690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357380690 none Cc1ccccc1NC(=O)[C@@H]1CCc2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', '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', '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, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 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, 4, 7, 6, 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] 0 hydrogens 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, 19, 35, 35, 19, 19, 5, 19, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 22, 35, 35, 19, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4] 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: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 21) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccccc1NC(=O)[C@@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001357380690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357380690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357380690 none Cc1ccccc1NC(=O)[C@@H]1CCc2ccccc2N1C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', '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', '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, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 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, 4, 7, 6, 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] 0 hydrogens 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, 24, 37, 37, 24, 24, 9, 24, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 37, 37, 37, 37, 25, 37, 37, 24, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5] 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: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357380690 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357380690 Building ZINC001357399374 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357399374 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/22 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(c2ccccc2)ccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001357399374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357399374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001357399374 none CCOC(=O)c1cc(c2ccccc2)ccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)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', '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', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 7, 20, 7, 7, 7, 7, 14, 14, 7, 14, 14, 7, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 7, 14, 14, 7, 14, 14, 7, 7, 2, 4, 4, 4, 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/23 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/23' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(c2ccccc2)ccc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001357399374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357399374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001357399374 none CCOC(=O)c1cc(c2ccccc2)ccc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)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', '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', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 7, 18, 7, 7, 7, 7, 14, 14, 7, 14, 14, 7, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 7, 14, 14, 7, 14, 14, 7, 7, 2, 4, 4, 4, 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357399374 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374 Building ZINC001357399374 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357399374 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 22) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCOC(=O)c1cc(c2ccccc2)ccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001357399374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357399374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001357399374 none CCOC(=O)c1cc(c2ccccc2)ccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)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', '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', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 7, 20, 7, 7, 7, 7, 14, 14, 7, 14, 14, 7, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 7, 14, 14, 7, 14, 14, 7, 7, 2, 4, 4, 4, 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 23) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCOC(=O)c1cc(c2ccccc2)ccc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001357399374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357399374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001357399374 none CCOC(=O)c1cc(c2ccccc2)ccc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)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', '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', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 7, 18, 7, 7, 7, 7, 14, 14, 7, 14, 14, 7, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 7, 14, 14, 7, 14, 14, 7, 7, 2, 4, 4, 4, 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357399374 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357399374 Building ZINC001357409688 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357409688 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/24 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/24' -> `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(c2cccc(C)c2)CCCCC1) `ZINC001357409688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357409688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001357409688 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(c2cccc(C)c2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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'] 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, 1, 5, 1, 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] dock 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, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 16, 24, 44, 44, 24, 44, 44, 44, 24, 24, 24, 24, 24, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 11, 11, 44, 44, 44, 44, 44, 44, 44, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/25 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/25' -> `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(c2cccc(C)c2)CCCCC1) `ZINC001357409688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357409688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001357409688 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(c2cccc(C)c2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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'] 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, 1, 5, 1, 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] dock 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, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 18, 25, 45, 45, 25, 45, 45, 45, 25, 25, 25, 25, 25, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 12, 12, 45, 45, 37, 45, 45, 45, 45, 25, 25, 25, 25, 25, 25, 25, 25, 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, 59, 60, 61, 62]) total number of confs: 208 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357409688 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688 Building ZINC001357409688 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357409688 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 24) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(c2cccc(C)c2)CCCCC1) `ZINC001357409688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357409688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001357409688 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(c2cccc(C)c2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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'] 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, 1, 5, 1, 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] dock 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, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 16, 24, 44, 44, 24, 44, 44, 44, 24, 24, 24, 24, 24, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 11, 11, 44, 44, 44, 44, 44, 44, 44, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 25) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(c2cccc(C)c2)CCCCC1) `ZINC001357409688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357409688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001357409688 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(c2cccc(C)c2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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'] 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, 1, 5, 1, 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] dock 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, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 18, 25, 45, 45, 25, 45, 45, 45, 25, 25, 25, 25, 25, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 12, 12, 45, 45, 37, 45, 45, 45, 45, 25, 25, 25, 25, 25, 25, 25, 25, 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, 59, 60, 61, 62]) total number of confs: 208 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357409688 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357409688 Building ZINC001357422596 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357422596 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/26 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cc1OCC) `ZINC001357422596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357422596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001357422596 none CCOc1cc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'O.3', 'C.3', 'C.3', '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, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 23, 5, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 5, 5, 5, 23, 29, 30, 30, 30, 30, 30, 5, 3, 6, 6, 5, 29, 29, 29, 29, 29] 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/27 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/27' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(Br)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cc1OCC) `ZINC001357422596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357422596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001357422596 none CCOc1cc(Br)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'O.3', 'C.3', 'C.3', '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, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 24, 5, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 5, 5, 5, 22, 29, 33, 33, 33, 33, 33, 5, 3, 7, 7, 5, 29, 29, 29, 29, 29] 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]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357422596 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596 Building ZINC001357422596 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357422596 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 26) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCOc1cc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cc1OCC) `ZINC001357422596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357422596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001357422596 none CCOc1cc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'O.3', 'C.3', 'C.3', '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, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 23, 5, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 5, 5, 5, 23, 29, 30, 30, 30, 30, 30, 5, 3, 6, 6, 5, 29, 29, 29, 29, 29] 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 27) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCOc1cc(Br)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cc1OCC) `ZINC001357422596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357422596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001357422596 none CCOc1cc(Br)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'O.3', 'C.3', 'C.3', '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, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 24, 5, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 5, 5, 5, 22, 29, 33, 33, 33, 33, 33, 5, 3, 7, 7, 5, 29, 29, 29, 29, 29] 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]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357422596 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357422596 Building ZINC001357440515 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357440515 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/28 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](c1ccc(Cl)cc1)N(CC)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001357440515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357440515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001357440515 none CCOC(=O)[C@H](c1ccc(Cl)cc1)N(CC)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 21, 8, 21, 5, 8, 8, 9, 9, 8, 8, 9, 9, 2, 5, 10, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 33, 33, 33, 33, 33, 9, 9, 9, 9, 10, 10, 10, 10, 10, 3, 1, 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]) total number of confs: 158 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/29 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/29' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](c1ccc(Cl)cc1)N(CC)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001357440515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357440515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001357440515 none CCOC(=O)[C@H](c1ccc(Cl)cc1)N(CC)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 31, 19, 31, 9, 19, 19, 20, 20, 19, 20, 20, 20, 4, 9, 13, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 45, 45, 45, 45, 45, 20, 20, 20, 20, 13, 13, 13, 13, 13, 4, 1, 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]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357440515 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515 Building ZINC001357440515 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357440515 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 28) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCOC(=O)[C@H](c1ccc(Cl)cc1)N(CC)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001357440515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357440515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001357440515 none CCOC(=O)[C@H](c1ccc(Cl)cc1)N(CC)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 21, 8, 21, 5, 8, 8, 9, 9, 8, 8, 9, 9, 2, 5, 10, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 33, 33, 33, 33, 33, 9, 9, 9, 9, 10, 10, 10, 10, 10, 3, 1, 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]) total number of confs: 158 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 29) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCOC(=O)[C@H](c1ccc(Cl)cc1)N(CC)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001357440515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357440515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001357440515 none CCOC(=O)[C@H](c1ccc(Cl)cc1)N(CC)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 31, 19, 31, 9, 19, 19, 20, 20, 19, 20, 20, 20, 4, 9, 13, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 45, 45, 45, 45, 45, 20, 20, 20, 20, 13, 13, 13, 13, 13, 4, 1, 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]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357440515 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440515 Building ZINC001357440516 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357440516 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/30 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](c1ccc(Cl)cc1)N(CC)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001357440516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357440516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001357440516 none CCOC(=O)[C@@H](c1ccc(Cl)cc1)N(CC)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 30, 19, 30, 9, 19, 19, 20, 20, 19, 20, 20, 20, 4, 9, 13, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 46, 46, 46, 46, 46, 20, 20, 20, 20, 13, 13, 13, 13, 13, 4, 2, 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]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/31 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/31' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](c1ccc(Cl)cc1)N(CC)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001357440516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357440516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001357440516 none CCOC(=O)[C@@H](c1ccc(Cl)cc1)N(CC)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 8, 21, 5, 8, 8, 9, 9, 8, 8, 9, 9, 2, 5, 10, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 32, 32, 32, 32, 32, 9, 9, 9, 9, 10, 10, 10, 10, 10, 3, 1, 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]) total number of confs: 157 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357440516 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516 Building ZINC001357440516 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357440516 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 30) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCOC(=O)[C@@H](c1ccc(Cl)cc1)N(CC)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001357440516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357440516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001357440516 none CCOC(=O)[C@@H](c1ccc(Cl)cc1)N(CC)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 30, 19, 30, 9, 19, 19, 20, 20, 19, 20, 20, 20, 4, 9, 13, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 46, 46, 46, 46, 46, 20, 20, 20, 20, 13, 13, 13, 13, 13, 4, 2, 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]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 31) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCOC(=O)[C@@H](c1ccc(Cl)cc1)N(CC)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001357440516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357440516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001357440516 none CCOC(=O)[C@@H](c1ccc(Cl)cc1)N(CC)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 8, 21, 5, 8, 8, 9, 9, 8, 8, 9, 9, 2, 5, 10, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 32, 32, 32, 32, 32, 9, 9, 9, 9, 10, 10, 10, 10, 10, 3, 1, 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]) total number of confs: 157 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357440516 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357440516 Building ZINC001357463419 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357463419 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/32 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CCCC[C@H]2C)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357463419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357463419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357463419 none Cc1cc(C(=O)N2CCCC[C@H]2C)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', 'Br', 'S.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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 9, 5, 9, 27, 27, 35, 35, 35, 35, 35, 35, 35, 9, 9, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 9, 9, 9, 9, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 9, 9, 3, 8, 8] 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/33 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/33' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CCCC[C@H]2C)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357463419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357463419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357463419 none Cc1cc(C(=O)N2CCCC[C@H]2C)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', 'Br', 'S.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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 4, 4, 25, 24, 34, 34, 34, 34, 34, 34, 34, 6, 6, 2, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 8, 6, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 6, 6, 2, 8, 8] 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357463419 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419 Building ZINC001357463419 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357463419 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 32) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(C(=O)N2CCCC[C@H]2C)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357463419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357463419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357463419 none Cc1cc(C(=O)N2CCCC[C@H]2C)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', 'Br', 'S.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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 9, 5, 9, 27, 27, 35, 35, 35, 35, 35, 35, 35, 9, 9, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 9, 9, 9, 9, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 9, 9, 3, 8, 8] 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 33) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(C(=O)N2CCCC[C@H]2C)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357463419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357463419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357463419 none Cc1cc(C(=O)N2CCCC[C@H]2C)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', 'Br', 'S.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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 4, 4, 25, 24, 34, 34, 34, 34, 34, 34, 34, 6, 6, 2, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 8, 6, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 6, 6, 2, 8, 8] 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357463419 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463419 Building ZINC001357463431 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357463431 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/34 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CCCC[C@@H]2C)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357463431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357463431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357463431 none Cc1cc(C(=O)N2CCCC[C@@H]2C)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', 'Br', 'S.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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 4, 6, 26, 26, 35, 35, 35, 35, 35, 35, 35, 6, 6, 2, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 8, 6, 6, 6, 6, 34, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 6, 6, 2, 8, 8] 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/35 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/35' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CCCC[C@@H]2C)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357463431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357463431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357463431 none Cc1cc(C(=O)N2CCCC[C@@H]2C)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', 'Br', 'S.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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 9, 3, 5, 27, 27, 35, 35, 35, 35, 35, 35, 35, 9, 9, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 9, 9, 9, 9, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 9, 9, 3, 8, 8] 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357463431 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431 Building ZINC001357463431 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357463431 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 34) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(C(=O)N2CCCC[C@@H]2C)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357463431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357463431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357463431 none Cc1cc(C(=O)N2CCCC[C@@H]2C)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', 'Br', 'S.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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 4, 6, 26, 26, 35, 35, 35, 35, 35, 35, 35, 6, 6, 2, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 8, 6, 6, 6, 6, 34, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 6, 6, 2, 8, 8] 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 35) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(C(=O)N2CCCC[C@@H]2C)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357463431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357463431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357463431 none Cc1cc(C(=O)N2CCCC[C@@H]2C)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', 'Br', 'S.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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 9, 3, 5, 27, 27, 35, 35, 35, 35, 35, 35, 35, 9, 9, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 9, 9, 9, 9, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 9, 9, 3, 8, 8] 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357463431 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357463431 Building ZINC001357467060 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357467060 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/36 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/36' -> `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)c1cccc(C)c1) `ZINC001357467060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357467060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001357467060 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1cccc(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.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type 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, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 8, 8, 8, 8, 8, 8, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 3, 5, 5, 5, 8, 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, 49, 50, 51, 52]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/37 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/37' -> `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)c1cccc(C)c1) `ZINC001357467060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357467060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001357467060 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1cccc(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.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type 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, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 5, 5, 5, 10, 10, 10, 10, 10, 10, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 5, 5, 5, 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]) total number of confs: 49 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357467060 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060 Building ZINC001357467060 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357467060 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 36) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/36: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)c1cccc(C)c1) `ZINC001357467060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357467060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001357467060 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1cccc(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.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type 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, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 8, 8, 8, 8, 8, 8, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 3, 5, 5, 5, 8, 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, 49, 50, 51, 52]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 37) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/37: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)c1cccc(C)c1) `ZINC001357467060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357467060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001357467060 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1cccc(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.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type 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, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 5, 5, 5, 10, 10, 10, 10, 10, 10, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 5, 5, 5, 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]) total number of confs: 49 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357467060 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467060 Building ZINC001357467381 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357467381 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/38 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(Br)c1) `ZINC001357467381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357467381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357467381 none CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 9, 15, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 15, 48, 48, 48, 48, 48, 48, 15, 15, 15, 15, 15, 15, 9, 9, 2, 3, 3, 48, 48, 48, 48] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/39 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/39' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(Br)c1) `ZINC001357467381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357467381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357467381 none CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 9, 15, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 15, 48, 48, 48, 48, 48, 48, 15, 15, 15, 15, 15, 15, 9, 9, 2, 3, 3, 48, 48, 48, 48] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357467381 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381 Building ZINC001357467381 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357467381 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 38) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(Br)c1) `ZINC001357467381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357467381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357467381 none CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 9, 15, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 15, 48, 48, 48, 48, 48, 48, 15, 15, 15, 15, 15, 15, 9, 9, 2, 3, 3, 48, 48, 48, 48] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 39) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(Br)c1) `ZINC001357467381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357467381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357467381 none CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 9, 15, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 15, 48, 48, 48, 48, 48, 48, 15, 15, 15, 15, 15, 15, 9, 9, 2, 3, 3, 48, 48, 48, 48] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357467381 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357467381 Building ZINC001357486094 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357486094 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/40 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(Cc2cccc(Br)c2)s1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001357486094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357486094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357486094 none O=C(Nc1ncc(Cc2cccc(Br)c2)s1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 1, 17, 1, 14, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 15, 28, 28, 28, 28, 28, 28, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 15, 15, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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, 41, 42, 43]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/41 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/41' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(Cc2cccc(Br)c2)s1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001357486094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357486094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357486094 none O=C(Nc1ncc(Cc2cccc(Br)c2)s1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 1, 17, 1, 14, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 15, 29, 29, 29, 29, 29, 29, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 15, 15, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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, 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/182395/xbh-8058088.34/working/building/ZINC001357486094 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357486094 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094 Building ZINC001357486094 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357486094 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 40) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Nc1ncc(Cc2cccc(Br)c2)s1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001357486094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357486094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357486094 none O=C(Nc1ncc(Cc2cccc(Br)c2)s1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 1, 17, 1, 14, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 15, 28, 28, 28, 28, 28, 28, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 15, 15, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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, 41, 42, 43]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 41) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Nc1ncc(Cc2cccc(Br)c2)s1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001357486094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357486094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357486094 none O=C(Nc1ncc(Cc2cccc(Br)c2)s1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 1, 17, 1, 14, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 15, 29, 29, 29, 29, 29, 29, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 15, 15, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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, 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/182395/xbh-8058088.34/working/building/ZINC001357486094 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357486094 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357486094 Building ZINC001357538777 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357538777 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/42 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@H]2CCc3ccccc3N2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cc1) `ZINC001357538777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357538777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001357538777 none Cc1ccc(NC(=O)[C@H]2CCc3ccccc3N2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)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', 'H', 'C.3', 'C.3', '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', 'C.2', 'C.2', 'Cl', 'S.3', '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, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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, 7, 4, 7, 6, 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] 0 hydrogens 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, 25, 25, 11, 25, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 2, 10, 1, 1, 1, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 25, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 31, 31] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/43 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/43' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@H]2CCc3ccccc3N2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cc1) `ZINC001357538777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357538777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001357538777 none Cc1ccc(NC(=O)[C@H]2CCc3ccccc3N2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)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', 'H', 'C.3', 'C.3', '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', 'C.2', 'C.2', 'Cl', 'S.3', '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, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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, 7, 4, 7, 6, 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] 0 hydrogens 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, 31, 31, 22, 22, 11, 22, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 2, 10, 1, 1, 1, 10, 10, 10, 10, 10, 31, 31, 31, 31, 31, 31, 31, 22, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 31, 31] 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]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357538777 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777 Building ZINC001357538777 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357538777 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 42) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(NC(=O)[C@H]2CCc3ccccc3N2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cc1) `ZINC001357538777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357538777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001357538777 none Cc1ccc(NC(=O)[C@H]2CCc3ccccc3N2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)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', 'H', 'C.3', 'C.3', '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', 'C.2', 'C.2', 'Cl', 'S.3', '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, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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, 7, 4, 7, 6, 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] 0 hydrogens 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, 25, 25, 11, 25, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 2, 10, 1, 1, 1, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 25, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 31, 31] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 43) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(NC(=O)[C@H]2CCc3ccccc3N2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cc1) `ZINC001357538777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357538777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001357538777 none Cc1ccc(NC(=O)[C@H]2CCc3ccccc3N2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)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', 'H', 'C.3', 'C.3', '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', 'C.2', 'C.2', 'Cl', 'S.3', '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, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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, 7, 4, 7, 6, 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] 0 hydrogens 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, 31, 31, 22, 22, 11, 22, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 2, 10, 1, 1, 1, 10, 10, 10, 10, 10, 31, 31, 31, 31, 31, 31, 31, 22, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 31, 31] 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]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357538777 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538777 Building ZINC001357538784 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357538784 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/44 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@H]2CCc3ccccc3N2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cc1) `ZINC001357538784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357538784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001357538784 none Cc1ccc(NC(=O)[C@@H]2CCc3ccccc3N2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)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', 'H', 'C.3', 'C.3', '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', 'C.2', 'C.2', 'Cl', 'S.3', '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, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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, 7, 4, 7, 6, 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] 0 hydrogens 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, 20, 20, 6, 20, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 2, 5, 1, 1, 1, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 20, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 24, 24] 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/45 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@H]2CCc3ccccc3N2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cc1) `ZINC001357538784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357538784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001357538784 none Cc1ccc(NC(=O)[C@@H]2CCc3ccccc3N2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)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', 'H', 'C.3', 'C.3', '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', 'C.2', 'C.2', 'Cl', 'S.3', '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, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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, 7, 4, 7, 6, 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] 0 hydrogens 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, 33, 33, 28, 28, 12, 28, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 12, 1, 1, 1, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 28, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9, 33, 33] 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357538784 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784 Building ZINC001357538784 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357538784 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 44) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/44: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H]2CCc3ccccc3N2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cc1) `ZINC001357538784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357538784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001357538784 none Cc1ccc(NC(=O)[C@@H]2CCc3ccccc3N2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)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', 'H', 'C.3', 'C.3', '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', 'C.2', 'C.2', 'Cl', 'S.3', '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, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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, 7, 4, 7, 6, 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] 0 hydrogens 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, 20, 20, 6, 20, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 2, 5, 1, 1, 1, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 20, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 24, 24] 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 45) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H]2CCc3ccccc3N2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cc1) `ZINC001357538784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357538784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001357538784 none Cc1ccc(NC(=O)[C@@H]2CCc3ccccc3N2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)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', 'H', 'C.3', 'C.3', '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', 'C.2', 'C.2', 'Cl', 'S.3', '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, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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, 7, 4, 7, 6, 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] 0 hydrogens 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, 33, 33, 28, 28, 12, 28, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 12, 1, 1, 1, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 28, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9, 33, 33] 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357538784 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357538784 Building ZINC001357541489 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357541489 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/46 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)OC(C)(C)C)ccc(C)c21) `ZINC001357541489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357541489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357541489 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)OC(C)(C)C)ccc(C)c21 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.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 5, 1, 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] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 4, 4, 20, 29, 29, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 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, 57]) total number of confs: 128 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/47 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/47' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)OC(C)(C)C)ccc(C)c21) `ZINC001357541489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357541489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357541489 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)OC(C)(C)C)ccc(C)c21 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.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 5, 1, 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] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 4, 4, 20, 30, 30, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 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, 57]) total number of confs: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357541489 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489 Building ZINC001357541489 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357541489 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 46) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)OC(C)(C)C)ccc(C)c21) `ZINC001357541489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357541489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357541489 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)OC(C)(C)C)ccc(C)c21 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.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 5, 1, 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] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 4, 4, 20, 29, 29, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 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, 57]) total number of confs: 128 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 47) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)OC(C)(C)C)ccc(C)c21) `ZINC001357541489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357541489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357541489 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)OC(C)(C)C)ccc(C)c21 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.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 5, 1, 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] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 4, 4, 20, 30, 30, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 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, 57]) total number of confs: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357541489 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357541489 Building ZINC001357576200 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357576200 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/48 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1OC) `ZINC001357576200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357576200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357576200 none CCCCOc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'Br', 'S.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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [50, 50, 24, 21, 6, 6, 6, 6, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 6, 11, 50, 50, 50, 50, 50, 50, 50, 24, 24, 6, 6, 4, 4, 4, 2, 2, 2, 6, 11, 11, 11] 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: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/49 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/49' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1OC) `ZINC001357576200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357576200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357576200 none CCCCOc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'Br', 'S.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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [50, 50, 28, 22, 7, 7, 7, 7, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 7, 13, 50, 50, 50, 50, 50, 50, 50, 28, 28, 7, 7, 3, 3, 3, 2, 2, 2, 7, 13, 13, 13] 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: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357576200 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200 Building ZINC001357576200 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357576200 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 48) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/48: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1OC) `ZINC001357576200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357576200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357576200 none CCCCOc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'Br', 'S.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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [50, 50, 24, 21, 6, 6, 6, 6, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 6, 11, 50, 50, 50, 50, 50, 50, 50, 24, 24, 6, 6, 4, 4, 4, 2, 2, 2, 6, 11, 11, 11] 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: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 49) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/49: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1OC) `ZINC001357576200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357576200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357576200 none CCCCOc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'Br', 'S.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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [50, 50, 28, 22, 7, 7, 7, 7, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 7, 13, 50, 50, 50, 50, 50, 50, 50, 28, 28, 7, 7, 3, 3, 3, 2, 2, 2, 7, 13, 13, 13] 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: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357576200 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576200 Building ZINC001357576201 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357576201 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/50 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1OC) `ZINC001357576201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357576201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357576201 none CCCCOc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'Br', 'S.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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [50, 50, 28, 22, 7, 7, 7, 7, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 7, 13, 50, 50, 50, 50, 50, 50, 50, 28, 28, 7, 7, 3, 3, 3, 2, 2, 2, 7, 13, 13, 13] 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: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/51 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1OC) `ZINC001357576201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357576201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357576201 none CCCCOc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'Br', 'S.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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [50, 50, 25, 21, 6, 6, 6, 6, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 6, 11, 50, 50, 50, 50, 50, 50, 50, 25, 25, 6, 6, 4, 4, 4, 2, 2, 2, 6, 11, 11, 11] 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357576201 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201 Building ZINC001357576201 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357576201 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 50) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCCOc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1OC) `ZINC001357576201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357576201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357576201 none CCCCOc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'Br', 'S.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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [50, 50, 28, 22, 7, 7, 7, 7, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 7, 13, 50, 50, 50, 50, 50, 50, 50, 28, 28, 7, 7, 3, 3, 3, 2, 2, 2, 7, 13, 13, 13] 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: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 51) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCCOc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1OC) `ZINC001357576201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357576201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357576201 none CCCCOc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'Br', 'S.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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [50, 50, 25, 21, 6, 6, 6, 6, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 6, 11, 50, 50, 50, 50, 50, 50, 50, 25, 25, 6, 6, 4, 4, 4, 2, 2, 2, 6, 11, 11, 11] 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357576201 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357576201 Building ZINC001357604681 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357604681 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/52 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCN1CCCCC1)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001357604681.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357604681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357604681 none O=C(CCN1CCCCC1)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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: [11, 1, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 34, 34, 50, 50, 50, 50, 50, 2, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 8, 8, 2, 2, 1, 2, 8, 8] 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: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/53 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/53' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCN1CCCCC1)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001357604681.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357604681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357604681 none O=C(CCN1CCCCC1)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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: [11, 1, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 33, 33, 50, 50, 50, 50, 50, 7, 6, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 7, 7, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 7, 7, 2, 2, 1, 2, 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]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357604681 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681 Building ZINC001357604681 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357604681 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 52) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(CCN1CCCCC1)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001357604681.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357604681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357604681 none O=C(CCN1CCCCC1)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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: [11, 1, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 34, 34, 50, 50, 50, 50, 50, 2, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 8, 8, 2, 2, 1, 2, 8, 8] 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: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 53) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(CCN1CCCCC1)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001357604681.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357604681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357604681 none O=C(CCN1CCCCC1)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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: [11, 1, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 33, 33, 50, 50, 50, 50, 50, 7, 6, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 7, 7, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 7, 7, 2, 2, 1, 2, 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]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357604681 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357604681 Building ZINC001357612909 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357612909 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/54 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(c2nnc3n2CCCCC3)ccc1F)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001357612909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357612909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001357612909 none O=C(Nc1cc(c2nnc3n2CCCCC3)ccc1F)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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: [11, 1, 8, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 1, 15, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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] 0 hydrogens 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, 16, 24, 39, 39, 24, 39, 39, 39, 39, 39, 13, 13, 13, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 13, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 13, 13, 3, 1, 3] 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/55 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/55' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(c2nnc3n2CCCCC3)ccc1F)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001357612909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357612909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001357612909 none O=C(Nc1cc(c2nnc3n2CCCCC3)ccc1F)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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: [11, 1, 8, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 1, 15, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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] 0 hydrogens 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, 16, 23, 38, 38, 23, 38, 38, 38, 38, 38, 13, 13, 13, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 13, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 13, 13, 3, 1, 3] 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357612909 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909 Building ZINC001357612909 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357612909 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 54) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cc(c2nnc3n2CCCCC3)ccc1F)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001357612909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357612909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001357612909 none O=C(Nc1cc(c2nnc3n2CCCCC3)ccc1F)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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: [11, 1, 8, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 1, 15, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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] 0 hydrogens 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, 16, 24, 39, 39, 24, 39, 39, 39, 39, 39, 13, 13, 13, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 13, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 13, 13, 3, 1, 3] 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 55) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cc(c2nnc3n2CCCCC3)ccc1F)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001357612909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357612909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001357612909 none O=C(Nc1cc(c2nnc3n2CCCCC3)ccc1F)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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: [11, 1, 8, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 1, 15, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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] 0 hydrogens 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, 16, 23, 38, 38, 23, 38, 38, 38, 38, 38, 13, 13, 13, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 13, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 13, 13, 3, 1, 3] 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357612909 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357612909 Building ZINC001357617401 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357617401 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/56 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCC)C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001357617401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357617401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001357617401 none CCCN(CCC)C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', '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.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 33, 20, 19, 20, 20, 33, 8, 20, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 42, 42, 42, 42, 42, 33, 33, 20, 20, 33, 33, 33, 33, 33, 11, 11, 2, 6, 6, 11, 11] 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]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/57 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/57' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCC)C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001357617401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357617401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001357617401 none CCCN(CCC)C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', '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.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 33, 20, 20, 20, 20, 33, 11, 20, 8, 11, 11, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 42, 42, 42, 42, 42, 33, 33, 20, 20, 33, 33, 33, 33, 33, 11, 11, 2, 5, 5, 11, 11] 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]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357617401 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401 Building ZINC001357617401 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357617401 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 56) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCN(CCC)C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001357617401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357617401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001357617401 none CCCN(CCC)C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', '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.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 33, 20, 19, 20, 20, 33, 8, 20, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 42, 42, 42, 42, 42, 33, 33, 20, 20, 33, 33, 33, 33, 33, 11, 11, 2, 6, 6, 11, 11] 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]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 57) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCN(CCC)C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001357617401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357617401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001357617401 none CCCN(CCC)C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', '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.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 33, 20, 20, 20, 20, 33, 11, 20, 8, 11, 11, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 42, 42, 42, 42, 42, 33, 33, 20, 20, 33, 33, 33, 33, 33, 11, 11, 2, 5, 5, 11, 11] 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]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357617401 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357617401 Building ZINC001357618301 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357618301 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/58 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)C(=O)c1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001357618301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357618301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357618301 none CC(C)N(C)C(=O)c1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 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, 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] 0 hydrogens 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, 46, 28, 42, 8, 28, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 46, 46, 46, 46, 46, 46, 46, 42, 42, 42, 8, 8, 3, 3, 1, 3, 8] 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: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/59 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/59' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)C(=O)c1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001357618301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357618301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357618301 none CC(C)N(C)C(=O)c1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 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, 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] 0 hydrogens 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, 41, 45, 26, 41, 9, 26, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 45, 45, 45, 45, 45, 45, 45, 41, 41, 41, 9, 9, 3, 3, 1, 3, 9] 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: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357618301 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301 Building ZINC001357618301 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357618301 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 58) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)N(C)C(=O)c1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001357618301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357618301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357618301 none CC(C)N(C)C(=O)c1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 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, 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] 0 hydrogens 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, 46, 28, 42, 8, 28, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 46, 46, 46, 46, 46, 46, 46, 42, 42, 42, 8, 8, 3, 3, 1, 3, 8] 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: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 59) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)N(C)C(=O)c1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001357618301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357618301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357618301 none CC(C)N(C)C(=O)c1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 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, 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] 0 hydrogens 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, 41, 45, 26, 41, 9, 26, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 45, 45, 45, 45, 45, 45, 45, 41, 41, 41, 9, 9, 3, 3, 1, 3, 9] 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: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357618301 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357618301 Building ZINC001357748957 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357748957 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/60 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCc2cc(Br)cc(F)c21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357748957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357748957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC001357748957 none O=C(N1CCCc2cc(Br)cc(F)c21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 17, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 8, 10, 11, 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: [9, 3, 15, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 9, 9] 33 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]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/61 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/61' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCc2cc(Br)cc(F)c21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357748957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357748957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC001357748957 none O=C(N1CCCc2cc(Br)cc(F)c21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 17, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 8, 10, 11, 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: [9, 3, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9] 34 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]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357748957 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957 Building ZINC001357748957 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357748957 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 60) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(N1CCCc2cc(Br)cc(F)c21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357748957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357748957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC001357748957 none O=C(N1CCCc2cc(Br)cc(F)c21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 17, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 8, 10, 11, 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: [9, 3, 15, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 9, 9] 33 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]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 61) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(N1CCCc2cc(Br)cc(F)c21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357748957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357748957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC001357748957 none O=C(N1CCCc2cc(Br)cc(F)c21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 17, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 8, 10, 11, 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: [9, 3, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9] 34 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]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357748957 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357748957 Building ZINC001357756791 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357756791 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/62 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)c(N2CCCCC2)c(F)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357756791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357756791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001357756791 none O=C(Nc1cc(F)c(N2CCCCC2)c(F)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 15, 1, 8, 5, 5, 5, 5, 5, 1, 15, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens 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, 10, 10, 10, 8, 14, 40, 40, 40, 40, 35, 10, 10, 10, 1, 1, 1, 9, 9, 9, 9, 9, 4, 10, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 10, 9, 9] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/63 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/63' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)c(N2CCCCC2)c(F)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357756791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357756791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001357756791 none O=C(Nc1cc(F)c(N2CCCCC2)c(F)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 15, 1, 8, 5, 5, 5, 5, 5, 1, 15, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens 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, 10, 10, 10, 10, 14, 41, 41, 41, 41, 36, 10, 10, 10, 1, 1, 1, 9, 9, 9, 9, 9, 4, 10, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 10, 9, 9] 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357756791 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791 Building ZINC001357756791 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357756791 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 62) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cc(F)c(N2CCCCC2)c(F)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357756791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357756791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001357756791 none O=C(Nc1cc(F)c(N2CCCCC2)c(F)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 15, 1, 8, 5, 5, 5, 5, 5, 1, 15, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens 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, 10, 10, 10, 8, 14, 40, 40, 40, 40, 35, 10, 10, 10, 1, 1, 1, 9, 9, 9, 9, 9, 4, 10, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 10, 9, 9] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 63) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cc(F)c(N2CCCCC2)c(F)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357756791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357756791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001357756791 none O=C(Nc1cc(F)c(N2CCCCC2)c(F)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 15, 1, 8, 5, 5, 5, 5, 5, 1, 15, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens 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, 10, 10, 10, 10, 14, 41, 41, 41, 41, 36, 10, 10, 10, 1, 1, 1, 9, 9, 9, 9, 9, 4, 10, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 10, 9, 9] 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357756791 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357756791 Building ZINC001357786736 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357786736 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/64 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@H](C)[C@@H]1C) `ZINC001357786736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357786736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001357786736 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@H](C)[C@@H]1C 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', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 10, 23, 23, 23, 23, 23, 23, 23, 23, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 10, 10, 23, 23, 23, 23, 23, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 29 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 7, 8, 9, 10, 39, 2, 3, 4, 6, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/65 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/65' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@H](C)[C@@H]1C) `ZINC001357786736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357786736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001357786736 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@H](C)[C@@H]1C 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', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 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, 8, 19, 19, 19, 19, 19, 19, 19, 19, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 8, 8, 19, 19, 19, 19, 19, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 22 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]) total number of confs: 59 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357786736 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736 Building ZINC001357786736 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357786736 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 64) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@H](C)[C@@H]1C) `ZINC001357786736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357786736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001357786736 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@H](C)[C@@H]1C 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', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 10, 23, 23, 23, 23, 23, 23, 23, 23, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 10, 10, 23, 23, 23, 23, 23, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 29 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 7, 8, 9, 10, 39, 2, 3, 4, 6, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 65) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@H](C)[C@@H]1C) `ZINC001357786736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357786736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001357786736 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@H](C)[C@@H]1C 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', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 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, 8, 19, 19, 19, 19, 19, 19, 19, 19, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 8, 8, 19, 19, 19, 19, 19, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 22 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]) total number of confs: 59 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357786736 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786736 Building ZINC001357786738 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357786738 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/66 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@@H](C)[C@@H]1C) `ZINC001357786738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357786738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001357786738 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@@H](C)[C@@H]1C 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', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 9, 19, 19, 19, 19, 19, 19, 19, 19, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 9, 9, 19, 19, 19, 19, 19, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 25 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 7, 8, 9, 10, 39, 2, 3, 4, 6, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 54 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/67 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/67' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@@H](C)[C@@H]1C) `ZINC001357786738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357786738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001357786738 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@@H](C)[C@@H]1C 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', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 5, 14, 14, 14, 14, 14, 14, 14, 14, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 5, 5, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 17 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]) total number of confs: 47 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357786738 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738 Building ZINC001357786738 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357786738 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 66) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@@H](C)[C@@H]1C) `ZINC001357786738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357786738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001357786738 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@@H](C)[C@@H]1C 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', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 9, 19, 19, 19, 19, 19, 19, 19, 19, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 9, 9, 19, 19, 19, 19, 19, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 25 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 7, 8, 9, 10, 39, 2, 3, 4, 6, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 54 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 67) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@@H](C)[C@@H]1C) `ZINC001357786738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357786738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001357786738 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@@H](C)[C@@H]1C 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', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 5, 14, 14, 14, 14, 14, 14, 14, 14, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 5, 5, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 17 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]) total number of confs: 47 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357786738 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786738 Building ZINC001357786743 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357786743 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/68 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@H](C)[C@H]1C) `ZINC001357786743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357786743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001357786743 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@H](C)[C@H]1C 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', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 7, 15, 30, 30, 30, 30, 30, 30, 30, 30, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 15, 15, 30, 30, 30, 30, 30, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 34 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]) total number of confs: 94 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/69 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/69' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@H](C)[C@H]1C) `ZINC001357786743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357786743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001357786743 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@H](C)[C@H]1C 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', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 6, 13, 26, 26, 26, 26, 26, 26, 26, 26, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 13, 13, 26, 26, 26, 26, 26, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 30 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]) total number of confs: 87 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357786743 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743 Building ZINC001357786743 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357786743 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 68) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@H](C)[C@H]1C) `ZINC001357786743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357786743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001357786743 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@H](C)[C@H]1C 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', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 7, 15, 30, 30, 30, 30, 30, 30, 30, 30, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 15, 15, 30, 30, 30, 30, 30, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 34 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]) total number of confs: 94 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 69) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@H](C)[C@H]1C) `ZINC001357786743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357786743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001357786743 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@H](C)[C@H]1C 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', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 6, 13, 26, 26, 26, 26, 26, 26, 26, 26, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 13, 13, 26, 26, 26, 26, 26, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 30 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]) total number of confs: 87 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357786743 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786743 Building ZINC001357786746 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357786746 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/70 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@@H](C)[C@H]1C) `ZINC001357786746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357786746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001357786746 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@@H](C)[C@H]1C 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', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 6, 10, 22, 22, 22, 22, 22, 22, 22, 22, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 10, 10, 22, 22, 22, 22, 22, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 35 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]) total number of confs: 76 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/71 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/71' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@@H](C)[C@H]1C) `ZINC001357786746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357786746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001357786746 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@@H](C)[C@H]1C 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', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 23, 23, 23, 23, 23, 23, 23, 23, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 10, 10, 23, 23, 23, 23, 23, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 29 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 7, 8, 9, 10, 39, 2, 3, 4, 6, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 77 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357786746 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746 Building ZINC001357786746 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357786746 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 70) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@@H](C)[C@H]1C) `ZINC001357786746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357786746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001357786746 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@@H](C)[C@H]1C 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', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 6, 10, 22, 22, 22, 22, 22, 22, 22, 22, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 10, 10, 22, 22, 22, 22, 22, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 35 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]) total number of confs: 76 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 71) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@@H](C)[C@H]1C) `ZINC001357786746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357786746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001357786746 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(Cc1ccc2c(c1)OCO2)[C@@H]1CCC[C@@H](C)[C@H]1C 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', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 23, 23, 23, 23, 23, 23, 23, 23, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 10, 10, 23, 23, 23, 23, 23, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 29 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 7, 8, 9, 10, 39, 2, 3, 4, 6, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 77 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357786746 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357786746 Building ZINC001357833741 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357833741 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/72 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1cnc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1) `ZINC001357833741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357833741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001357833741 none CCCc1cnc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', '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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 5, 5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 4, 13, 13, 13, 13, 13, 11, 11, 4, 2, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/73 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/73' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1cnc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1) `ZINC001357833741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357833741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001357833741 none CCCc1cnc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', '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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 5, 5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 4, 12, 12, 12, 12, 12, 10, 10, 4, 2, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2] 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357833741 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741 Building ZINC001357833741 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357833741 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 72) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCc1cnc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1) `ZINC001357833741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357833741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001357833741 none CCCc1cnc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', '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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 5, 5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 4, 13, 13, 13, 13, 13, 11, 11, 4, 2, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 73) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCc1cnc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1) `ZINC001357833741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357833741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001357833741 none CCCc1cnc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', '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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 5, 5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 4, 12, 12, 12, 12, 12, 10, 10, 4, 2, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2] 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357833741 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357833741 Building ZINC001357861861 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357861861 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/74 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)Nc1ccccc1) `ZINC001357861861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357861861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001357861861 none O=C(COc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)Nc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [45, 39, 37, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 45, 45, 49, 49, 45, 49, 49, 39, 39, 8, 8, 8, 2, 3, 1, 3, 8, 45, 49, 49, 48, 49, 49] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/75 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/75' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COc1cccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)Nc1ccccc1) `ZINC001357861861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357861861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001357861861 none O=C(COc1cccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)Nc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [45, 40, 38, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 45, 45, 49, 49, 45, 49, 49, 40, 40, 8, 8, 8, 2, 3, 1, 3, 8, 45, 49, 49, 49, 49, 49] 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357861861 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861 Building ZINC001357861861 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357861861 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 74) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(COc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)Nc1ccccc1) `ZINC001357861861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357861861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001357861861 none O=C(COc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)Nc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [45, 39, 37, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 45, 45, 49, 49, 45, 49, 49, 39, 39, 8, 8, 8, 2, 3, 1, 3, 8, 45, 49, 49, 48, 49, 49] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 75) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(COc1cccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)Nc1ccccc1) `ZINC001357861861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357861861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001357861861 none O=C(COc1cccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)Nc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [45, 40, 38, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 45, 45, 49, 49, 45, 49, 49, 40, 40, 8, 8, 8, 2, 3, 1, 3, 8, 45, 49, 49, 49, 49, 49] 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357861861 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357861861 Building ZINC001357922656 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357922656 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/76 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ncc(Cc2cccc(Br)c2)s1) `ZINC001357922656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357922656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001357922656 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ncc(Cc2cccc(Br)c2)s1 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.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', '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, 1, 8, 1, 1, 5, 1, 1, 1, 1, 1, 17, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 27, 50, 50, 50, 50, 50, 50, 6, 2, 2, 2, 2, 2, 2, 3, 6, 27, 27, 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/77 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/77' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ncc(Cc2cccc(Br)c2)s1) `ZINC001357922656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357922656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001357922656 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ncc(Cc2cccc(Br)c2)s1 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.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', '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, 1, 8, 1, 1, 5, 1, 1, 1, 1, 1, 17, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 28, 50, 50, 50, 50, 50, 50, 6, 2, 2, 2, 2, 2, 2, 3, 6, 28, 28, 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357922656 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656 Building ZINC001357922656 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357922656 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 76) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ncc(Cc2cccc(Br)c2)s1) `ZINC001357922656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357922656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001357922656 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ncc(Cc2cccc(Br)c2)s1 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.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', '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, 1, 8, 1, 1, 5, 1, 1, 1, 1, 1, 17, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 27, 50, 50, 50, 50, 50, 50, 6, 2, 2, 2, 2, 2, 2, 3, 6, 27, 27, 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 77) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ncc(Cc2cccc(Br)c2)s1) `ZINC001357922656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357922656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001357922656 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ncc(Cc2cccc(Br)c2)s1 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.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', '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, 1, 8, 1, 1, 5, 1, 1, 1, 1, 1, 17, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 28, 50, 50, 50, 50, 50, 50, 6, 2, 2, 2, 2, 2, 2, 3, 6, 28, 28, 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357922656 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357922656 Building ZINC001357959422 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001357959422 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/78 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357959422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357959422 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [11, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 22, 26, 26, 26, 26, 26, 12, 11, 11, 11, 11, 11, 10, 10, 6, 6, 12, 12, 12, 12, 12, 12, 22, 22, 26, 26, 26, 26, 26, 12, 12] 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]) total number of confs: 133 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/79 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/79' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357959422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357959422 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [11, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 22, 26, 26, 26, 26, 26, 12, 11, 11, 11, 11, 11, 10, 10, 6, 6, 12, 12, 12, 12, 12, 12, 22, 22, 26, 26, 26, 26, 26, 12, 12] 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]) total number of confs: 133 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/80 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/80' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959422.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001357959422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/2/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001357959422 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [11, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 18, 23, 23, 18, 23, 23, 9, 11, 11, 11, 11, 11, 10, 10, 6, 6, 9, 9, 9, 9, 9, 9, 18, 18, 23, 23, 18, 23, 23, 9, 9] 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]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/81 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/81' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959422.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001357959422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/3/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001357959422 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [11, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 18, 23, 23, 18, 23, 23, 9, 11, 11, 11, 11, 11, 10, 10, 6, 6, 9, 9, 9, 9, 9, 9, 18, 18, 23, 23, 18, 23, 23, 9, 9] 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]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357959422 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 Building ZINC001357959422 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001357959422 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 78) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/78: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357959422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357959422 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [11, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 22, 26, 26, 26, 26, 26, 12, 11, 11, 11, 11, 11, 10, 10, 6, 6, 12, 12, 12, 12, 12, 12, 22, 22, 26, 26, 26, 26, 26, 12, 12] 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]) total number of confs: 133 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 79) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/79: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357959422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357959422 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [11, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 22, 26, 26, 26, 26, 26, 12, 11, 11, 11, 11, 11, 10, 10, 6, 6, 12, 12, 12, 12, 12, 12, 22, 22, 26, 26, 26, 26, 26, 12, 12] 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]) total number of confs: 133 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 80) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/80: 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: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959422.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001357959422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/2/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001357959422 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [11, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 18, 23, 23, 18, 23, 23, 9, 11, 11, 11, 11, 11, 10, 10, 6, 6, 9, 9, 9, 9, 9, 9, 18, 18, 23, 23, 18, 23, 23, 9, 9] 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]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 81) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/81: 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: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959422.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001357959422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/3/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001357959422 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [11, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 18, 23, 23, 18, 23, 23, 9, 11, 11, 11, 11, 11, 10, 10, 6, 6, 9, 9, 9, 9, 9, 9, 18, 18, 23, 23, 18, 23, 23, 9, 9] 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]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357959422 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 Building ZINC001357959422 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001357959422 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 78) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/78: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357959422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357959422 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [11, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 22, 26, 26, 26, 26, 26, 12, 11, 11, 11, 11, 11, 10, 10, 6, 6, 12, 12, 12, 12, 12, 12, 22, 22, 26, 26, 26, 26, 26, 12, 12] 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]) total number of confs: 133 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 79) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/79: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357959422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357959422 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [11, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 22, 26, 26, 26, 26, 26, 12, 11, 11, 11, 11, 11, 10, 10, 6, 6, 12, 12, 12, 12, 12, 12, 22, 22, 26, 26, 26, 26, 26, 12, 12] 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]) total number of confs: 133 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 80) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/80: 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: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959422.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001357959422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/2/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001357959422 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [11, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 18, 23, 23, 18, 23, 23, 9, 11, 11, 11, 11, 11, 10, 10, 6, 6, 9, 9, 9, 9, 9, 9, 18, 18, 23, 23, 18, 23, 23, 9, 9] 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]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 81) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/81: 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: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959422.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001357959422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/3/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001357959422 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [11, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 18, 23, 23, 18, 23, 23, 9, 11, 11, 11, 11, 11, 10, 10, 6, 6, 9, 9, 9, 9, 9, 9, 18, 18, 23, 23, 18, 23, 23, 9, 9] 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]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357959422 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 Building ZINC001357959422 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001357959422 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 78) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/78: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357959422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357959422 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [11, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 22, 26, 26, 26, 26, 26, 12, 11, 11, 11, 11, 11, 10, 10, 6, 6, 12, 12, 12, 12, 12, 12, 22, 22, 26, 26, 26, 26, 26, 12, 12] 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]) total number of confs: 133 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 79) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/79: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357959422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357959422 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [11, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 22, 26, 26, 26, 26, 26, 12, 11, 11, 11, 11, 11, 10, 10, 6, 6, 12, 12, 12, 12, 12, 12, 22, 22, 26, 26, 26, 26, 26, 12, 12] 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]) total number of confs: 133 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 80) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/80: 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: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959422.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001357959422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/2/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001357959422 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [11, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 18, 23, 23, 18, 23, 23, 9, 11, 11, 11, 11, 11, 10, 10, 6, 6, 9, 9, 9, 9, 9, 9, 18, 18, 23, 23, 18, 23, 23, 9, 9] 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]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 81) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/81: 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: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959422.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001357959422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/3/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001357959422 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [11, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 18, 23, 23, 18, 23, 23, 9, 11, 11, 11, 11, 11, 10, 10, 6, 6, 9, 9, 9, 9, 9, 9, 18, 18, 23, 23, 18, 23, 23, 9, 9] 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]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357959422 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959422 Building ZINC001357959423 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001357959423 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/82 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357959423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357959423 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [9, 8, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 17, 23, 23, 22, 23, 23, 7, 9, 9, 9, 9, 9, 8, 8, 6, 6, 7, 7, 7, 7, 7, 7, 17, 17, 23, 23, 23, 23, 23, 7, 7] 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]) total number of confs: 112 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/83 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/83' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357959423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357959423 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [9, 8, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 17, 23, 23, 22, 23, 23, 7, 9, 9, 9, 9, 9, 8, 8, 6, 6, 7, 7, 7, 7, 7, 7, 17, 17, 23, 23, 23, 23, 23, 7, 7] 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]) total number of confs: 112 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/84 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/84' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959423.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001357959423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/2/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001357959423 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [10, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 10, 10, 10, 10, 10, 10, 19, 24, 24, 20, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 10, 10, 10, 10, 10, 10, 19, 19, 24, 24, 24, 24, 24, 10, 10] 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]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/85 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/85' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959423.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001357959423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/3/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001357959423 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [10, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 10, 10, 10, 10, 10, 10, 19, 24, 24, 20, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 10, 10, 10, 10, 10, 10, 19, 19, 24, 24, 24, 24, 24, 10, 10] 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]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357959423 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 Building ZINC001357959423 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001357959423 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 82) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/82: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357959423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357959423 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [9, 8, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 17, 23, 23, 22, 23, 23, 7, 9, 9, 9, 9, 9, 8, 8, 6, 6, 7, 7, 7, 7, 7, 7, 17, 17, 23, 23, 23, 23, 23, 7, 7] 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]) total number of confs: 112 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 83) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/83: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357959423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357959423 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [9, 8, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 17, 23, 23, 22, 23, 23, 7, 9, 9, 9, 9, 9, 8, 8, 6, 6, 7, 7, 7, 7, 7, 7, 17, 17, 23, 23, 23, 23, 23, 7, 7] 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]) total number of confs: 112 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 84) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/84: 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: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959423.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001357959423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/2/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001357959423 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [10, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 10, 10, 10, 10, 10, 10, 19, 24, 24, 20, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 10, 10, 10, 10, 10, 10, 19, 19, 24, 24, 24, 24, 24, 10, 10] 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]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 85) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/85: 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: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959423.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001357959423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/3/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001357959423 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [10, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 10, 10, 10, 10, 10, 10, 19, 24, 24, 20, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 10, 10, 10, 10, 10, 10, 19, 19, 24, 24, 24, 24, 24, 10, 10] 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]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357959423 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 Building ZINC001357959423 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001357959423 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 82) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/82: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357959423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357959423 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [9, 8, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 17, 23, 23, 22, 23, 23, 7, 9, 9, 9, 9, 9, 8, 8, 6, 6, 7, 7, 7, 7, 7, 7, 17, 17, 23, 23, 23, 23, 23, 7, 7] 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]) total number of confs: 112 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 83) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/83: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357959423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357959423 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [9, 8, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 17, 23, 23, 22, 23, 23, 7, 9, 9, 9, 9, 9, 8, 8, 6, 6, 7, 7, 7, 7, 7, 7, 17, 17, 23, 23, 23, 23, 23, 7, 7] 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]) total number of confs: 112 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 84) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/84: 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: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959423.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001357959423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/2/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001357959423 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [10, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 10, 10, 10, 10, 10, 10, 19, 24, 24, 20, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 10, 10, 10, 10, 10, 10, 19, 19, 24, 24, 24, 24, 24, 10, 10] 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]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 85) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/85: 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: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959423.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001357959423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/3/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001357959423 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [10, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 10, 10, 10, 10, 10, 10, 19, 24, 24, 20, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 10, 10, 10, 10, 10, 10, 19, 19, 24, 24, 24, 24, 24, 10, 10] 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]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357959423 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 Building ZINC001357959423 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001357959423 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 82) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/82: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357959423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357959423 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [9, 8, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 17, 23, 23, 22, 23, 23, 7, 9, 9, 9, 9, 9, 8, 8, 6, 6, 7, 7, 7, 7, 7, 7, 17, 17, 23, 23, 23, 23, 23, 7, 7] 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]) total number of confs: 112 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 83) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/83: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357959423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357959423 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [9, 8, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 17, 23, 23, 22, 23, 23, 7, 9, 9, 9, 9, 9, 8, 8, 6, 6, 7, 7, 7, 7, 7, 7, 17, 17, 23, 23, 23, 23, 23, 7, 7] 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]) total number of confs: 112 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 84) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/84: 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: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959423.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001357959423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/2/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001357959423 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [10, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 10, 10, 10, 10, 10, 10, 19, 24, 24, 20, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 10, 10, 10, 10, 10, 10, 19, 19, 24, 24, 24, 24, 24, 10, 10] 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]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 85) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/85: 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: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1) `ZINC001357959423.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001357959423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/3/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001357959423 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 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] dock color type numbers: [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: [10, 10, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 10, 10, 10, 10, 10, 10, 19, 24, 24, 20, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 10, 10, 10, 10, 10, 10, 19, 19, 24, 24, 24, 24, 24, 10, 10] 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]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357959423 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357959423 Building ZINC001357977041 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001357977041 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/86 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)cc2)cc1Cl) `ZINC001357977041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357977041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357977041 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)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.2', 'S.3', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 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] 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] 0 hydrogens 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, 2, 4, 4, 2, 7, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 9, 9, 9, 4, 4, 2, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/87 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/87' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)cc2)cc1Cl) `ZINC001357977041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357977041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357977041 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)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.2', 'S.3', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 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] 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] 0 hydrogens 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, 2, 4, 4, 2, 4, 26, 26, 26, 26, 26, 26, 26, 23, 4, 4, 4, 4, 4, 7, 7, 7, 4, 4, 2, 4, 4, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/88 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/88' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)cc2)cc1Cl) `ZINC001357977041.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001357977041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/2/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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357977041 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)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.2', 'S.3', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 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] 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] 0 hydrogens 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, 2, 4, 4, 2, 7, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 9, 9, 9, 4, 4, 2, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/89 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/89' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)cc2)cc1Cl) `ZINC001357977041.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001357977041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/3/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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357977041 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)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.2', 'S.3', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 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] 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] 0 hydrogens 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, 2, 4, 4, 2, 4, 26, 26, 26, 26, 26, 26, 26, 23, 4, 4, 4, 4, 4, 7, 7, 7, 4, 4, 2, 4, 4, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357977041 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 Building ZINC001357977041 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001357977041 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 86) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)cc2)cc1Cl) `ZINC001357977041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357977041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357977041 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)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.2', 'S.3', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 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] 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] 0 hydrogens 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, 2, 4, 4, 2, 7, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 9, 9, 9, 4, 4, 2, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 87) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)cc2)cc1Cl) `ZINC001357977041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357977041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357977041 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)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.2', 'S.3', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 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] 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] 0 hydrogens 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, 2, 4, 4, 2, 4, 26, 26, 26, 26, 26, 26, 26, 23, 4, 4, 4, 4, 4, 7, 7, 7, 4, 4, 2, 4, 4, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 88) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/88: 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(N3CCc4sccc4C3)cc2)cc1Cl) `ZINC001357977041.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001357977041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/2/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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357977041 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)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.2', 'S.3', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 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] 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] 0 hydrogens 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, 2, 4, 4, 2, 7, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 9, 9, 9, 4, 4, 2, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 89) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/89: 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(N3CCc4sccc4C3)cc2)cc1Cl) `ZINC001357977041.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001357977041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/3/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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357977041 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)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.2', 'S.3', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 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] 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] 0 hydrogens 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, 2, 4, 4, 2, 4, 26, 26, 26, 26, 26, 26, 26, 23, 4, 4, 4, 4, 4, 7, 7, 7, 4, 4, 2, 4, 4, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357977041 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 Building ZINC001357977041 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001357977041 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 86) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)cc2)cc1Cl) `ZINC001357977041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357977041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357977041 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)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.2', 'S.3', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 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] 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] 0 hydrogens 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, 2, 4, 4, 2, 7, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 9, 9, 9, 4, 4, 2, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 87) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)cc2)cc1Cl) `ZINC001357977041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357977041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357977041 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)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.2', 'S.3', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 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] 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] 0 hydrogens 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, 2, 4, 4, 2, 4, 26, 26, 26, 26, 26, 26, 26, 23, 4, 4, 4, 4, 4, 7, 7, 7, 4, 4, 2, 4, 4, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 88) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/88: 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(N3CCc4sccc4C3)cc2)cc1Cl) `ZINC001357977041.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001357977041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/2/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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357977041 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)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.2', 'S.3', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 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] 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] 0 hydrogens 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, 2, 4, 4, 2, 7, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 9, 9, 9, 4, 4, 2, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 89) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/89: 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(N3CCc4sccc4C3)cc2)cc1Cl) `ZINC001357977041.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001357977041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/3/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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357977041 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)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.2', 'S.3', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 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] 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] 0 hydrogens 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, 2, 4, 4, 2, 4, 26, 26, 26, 26, 26, 26, 26, 23, 4, 4, 4, 4, 4, 7, 7, 7, 4, 4, 2, 4, 4, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357977041 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 Building ZINC001357977041 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001357977041 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 86) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)cc2)cc1Cl) `ZINC001357977041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357977041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357977041 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)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.2', 'S.3', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 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] 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] 0 hydrogens 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, 2, 4, 4, 2, 7, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 9, 9, 9, 4, 4, 2, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 87) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)cc2)cc1Cl) `ZINC001357977041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357977041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357977041 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)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.2', 'S.3', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 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] 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] 0 hydrogens 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, 2, 4, 4, 2, 4, 26, 26, 26, 26, 26, 26, 26, 23, 4, 4, 4, 4, 4, 7, 7, 7, 4, 4, 2, 4, 4, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 88) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/88: 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(N3CCc4sccc4C3)cc2)cc1Cl) `ZINC001357977041.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001357977041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/2/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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357977041 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)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.2', 'S.3', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 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] 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] 0 hydrogens 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, 2, 4, 4, 2, 7, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 9, 9, 9, 4, 4, 2, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 89) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/89: 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(N3CCc4sccc4C3)cc2)cc1Cl) `ZINC001357977041.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001357977041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/3/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 51 natoms 50 natoms 49 natoms 48 names: ZINC001357977041 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(N3CCc4sccc4C3)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.2', 'S.3', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 14, 1, 1, 1, 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] 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] 0 hydrogens 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, 2, 4, 4, 2, 4, 26, 26, 26, 26, 26, 26, 26, 23, 4, 4, 4, 4, 4, 7, 7, 7, 4, 4, 2, 4, 4, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357977041 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357977041 Building ZINC001357986212 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357986212 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/90 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1NC(=O)c1ccncc1) `ZINC001357986212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357986212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357986212 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1NC(=O)c1ccncc1 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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 17, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 34, 34, 34, 43, 43, 34, 43, 43, 17, 17, 17, 17, 17, 4, 3, 1, 3, 17, 34, 43, 43, 43, 43] 50 rigid atoms, others: [6, 8, 9, 10] 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/91 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/91' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1NC(=O)c1ccncc1) `ZINC001357986212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357986212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357986212 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1NC(=O)c1ccncc1 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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 17, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 36, 36, 36, 42, 42, 36, 42, 42, 17, 17, 17, 17, 17, 4, 3, 1, 3, 17, 36, 42, 42, 42, 42] 50 rigid atoms, others: [6, 8, 9, 10] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357986212 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212 Building ZINC001357986212 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357986212 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 90) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1NC(=O)c1ccncc1) `ZINC001357986212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357986212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357986212 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1NC(=O)c1ccncc1 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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 17, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 34, 34, 34, 43, 43, 34, 43, 43, 17, 17, 17, 17, 17, 4, 3, 1, 3, 17, 34, 43, 43, 43, 43] 50 rigid atoms, others: [6, 8, 9, 10] 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 91) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1NC(=O)c1ccncc1) `ZINC001357986212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357986212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001357986212 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1NC(=O)c1ccncc1 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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 17, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 36, 36, 36, 42, 42, 36, 42, 42, 17, 17, 17, 17, 17, 4, 3, 1, 3, 17, 36, 42, 42, 42, 42] 50 rigid atoms, others: [6, 8, 9, 10] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357986212 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357986212 Building ZINC001357992693 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357992693 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/92 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/92' -> `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)c1cc(Cl)ccc1OC(F)F) `ZINC001357992693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357992693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001357992693 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1cc(Cl)ccc1OC(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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] 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, 16, 1, 1, 1, 12, 5, 15, 15, 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, 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, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 15, 15, 15, 10, 15, 15, 15, 28, 39, 39, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 3, 6, 6, 6, 15, 15, 15, 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]) total number of confs: 156 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/93 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/93' -> `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)c1cc(Cl)ccc1OC(F)F) `ZINC001357992693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357992693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001357992693 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1cc(Cl)ccc1OC(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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] 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, 16, 1, 1, 1, 12, 5, 15, 15, 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, 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, 9, 9, 5, 9, 9, 3, 3, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 27, 32, 32, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 4, 7, 7, 7, 18, 18, 18, 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]) total number of confs: 110 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357992693 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693 Building ZINC001357992693 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357992693 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 92) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1cc(Cl)ccc1OC(F)F) `ZINC001357992693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357992693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001357992693 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1cc(Cl)ccc1OC(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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] 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, 16, 1, 1, 1, 12, 5, 15, 15, 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, 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, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 15, 15, 15, 10, 15, 15, 15, 28, 39, 39, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 3, 6, 6, 6, 15, 15, 15, 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]) total number of confs: 156 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 93) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1cc(Cl)ccc1OC(F)F) `ZINC001357992693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357992693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001357992693 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1cc(Cl)ccc1OC(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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] 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, 16, 1, 1, 1, 12, 5, 15, 15, 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, 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, 9, 9, 5, 9, 9, 3, 3, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 27, 32, 32, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 4, 7, 7, 7, 18, 18, 18, 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]) total number of confs: 110 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357992693 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357992693 Building ZINC001357996446 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357996446 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/94 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/94' -> `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)Nc1cc(Cl)ccc1N1CCCCC1) `ZINC001357996446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357996446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001357996446 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 8, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 18, 30, 30, 30, 30, 30, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 6, 13, 13, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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: 82 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/95 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/95' -> `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)Nc1cc(Cl)ccc1N1CCCCC1) `ZINC001357996446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357996446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001357996446 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 8, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 5, 10, 10, 3, 3, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 11, 13, 13, 18, 30, 30, 30, 30, 29, 3, 3, 3, 10, 10, 5, 10, 10, 3, 3, 3, 6, 13, 13, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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: 95 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357996446 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446 Building ZINC001357996446 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357996446 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 94) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1N1CCCCC1) `ZINC001357996446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357996446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001357996446 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 8, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 18, 30, 30, 30, 30, 30, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 6, 13, 13, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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: 82 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 95) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1N1CCCCC1) `ZINC001357996446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357996446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001357996446 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 8, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 5, 10, 10, 3, 3, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 11, 13, 13, 18, 30, 30, 30, 30, 29, 3, 3, 3, 10, 10, 5, 10, 10, 3, 3, 3, 6, 13, 13, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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: 95 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357996446 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357996446 Building ZINC001357997835 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357997835 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/96 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)ccc1N1CCCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357997835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357997835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001357997835 none O=C(Nc1cc(Cl)ccc1N1CCCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 16, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 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: [4, 1, 4, 4, 11, 11, 11, 4, 11, 11, 18, 29, 29, 29, 29, 29, 1, 1, 1, 9, 9, 9, 9, 9, 4, 11, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/97 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/97' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)ccc1N1CCCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357997835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357997835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001357997835 none O=C(Nc1cc(Cl)ccc1N1CCCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 16, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 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: [4, 1, 4, 4, 11, 11, 11, 11, 11, 11, 18, 30, 30, 30, 30, 30, 1, 1, 1, 9, 9, 9, 9, 9, 4, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 9, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357997835 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835 Building ZINC001357997835 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357997835 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 96) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cc(Cl)ccc1N1CCCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357997835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357997835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001357997835 none O=C(Nc1cc(Cl)ccc1N1CCCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 16, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 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: [4, 1, 4, 4, 11, 11, 11, 4, 11, 11, 18, 29, 29, 29, 29, 29, 1, 1, 1, 9, 9, 9, 9, 9, 4, 11, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 97) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cc(Cl)ccc1N1CCCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001357997835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357997835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001357997835 none O=C(Nc1cc(Cl)ccc1N1CCCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 16, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 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: [4, 1, 4, 4, 11, 11, 11, 11, 11, 11, 18, 30, 30, 30, 30, 30, 1, 1, 1, 9, 9, 9, 9, 9, 4, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 9, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001357997835 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001357997835 Building ZINC001358011844 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358011844 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/98 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CCC[C@@H](C)C2)ccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001358011844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358011844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001358011844 none Cc1cc(C(=O)N2CCC[C@@H](C)C2)ccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 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: [7, 7, 7, 4, 7, 36, 36, 44, 44, 44, 44, 44, 44, 44, 7, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 7, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 7, 7, 2, 3, 1, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/99 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/99' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CCC[C@@H](C)C2)ccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001358011844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358011844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001358011844 none Cc1cc(C(=O)N2CCC[C@@H](C)C2)ccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 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: [8, 8, 8, 8, 8, 37, 37, 44, 44, 44, 44, 44, 44, 44, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 8, 8, 3, 3, 1, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358011844 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844 Building ZINC001358011844 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358011844 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 98) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(C(=O)N2CCC[C@@H](C)C2)ccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001358011844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358011844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001358011844 none Cc1cc(C(=O)N2CCC[C@@H](C)C2)ccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 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: [7, 7, 7, 4, 7, 36, 36, 44, 44, 44, 44, 44, 44, 44, 7, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 7, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 7, 7, 2, 3, 1, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 99) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(C(=O)N2CCC[C@@H](C)C2)ccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001358011844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358011844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001358011844 none Cc1cc(C(=O)N2CCC[C@@H](C)C2)ccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 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: [8, 8, 8, 8, 8, 37, 37, 44, 44, 44, 44, 44, 44, 44, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 8, 8, 3, 3, 1, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358011844 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011844 Building ZINC001358011845 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358011845 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/100 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CCC[C@H](C)C2)ccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001358011845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358011845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001358011845 none Cc1cc(C(=O)N2CCC[C@H](C)C2)ccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 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: [8, 8, 8, 3, 5, 35, 35, 45, 45, 45, 43, 43, 43, 43, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 45, 45, 45, 45, 45, 45, 43, 43, 43, 43, 43, 8, 8, 3, 3, 1, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/101 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/101' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CCC[C@H](C)C2)ccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001358011845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358011845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001358011845 none Cc1cc(C(=O)N2CCC[C@H](C)C2)ccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 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: [7, 7, 7, 2, 8, 34, 34, 43, 43, 43, 43, 43, 43, 42, 7, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 7, 43, 43, 43, 43, 43, 43, 40, 42, 43, 40, 42, 7, 7, 2, 3, 1, 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358011845 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845 Building ZINC001358011845 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358011845 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 100) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(C(=O)N2CCC[C@H](C)C2)ccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001358011845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358011845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001358011845 none Cc1cc(C(=O)N2CCC[C@H](C)C2)ccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 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: [8, 8, 8, 3, 5, 35, 35, 45, 45, 45, 43, 43, 43, 43, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 45, 45, 45, 45, 45, 45, 43, 43, 43, 43, 43, 8, 8, 3, 3, 1, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 101) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(C(=O)N2CCC[C@H](C)C2)ccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001358011845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358011845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001358011845 none Cc1cc(C(=O)N2CCC[C@H](C)C2)ccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 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: [7, 7, 7, 2, 8, 34, 34, 43, 43, 43, 43, 43, 43, 42, 7, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 7, 43, 43, 43, 43, 43, 43, 40, 42, 43, 40, 42, 7, 7, 2, 3, 1, 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358011845 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358011845 Building ZINC001358017341 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358017341 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/102 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1ccccc1)c1ccc(Br)cc1F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001358017341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358017341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001358017341 none O=C(N[C@@H](c1ccccc1)c1ccc(Br)cc1F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 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] 0 hydrogens 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, 6, 6, 11, 11, 26, 26, 11, 26, 26, 11, 39, 39, 19, 39, 39, 39, 39, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 26, 26, 11, 26, 26, 39, 39, 39, 3, 3, 3, 3] 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]) total number of confs: 216 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/103 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/103' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1ccccc1)c1ccc(Br)cc1F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001358017341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358017341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001358017341 none O=C(N[C@@H](c1ccccc1)c1ccc(Br)cc1F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 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] 0 hydrogens 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, 10, 10, 24, 24, 10, 24, 24, 10, 40, 40, 19, 40, 40, 40, 40, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 24, 24, 10, 24, 24, 40, 40, 40, 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]) total number of confs: 221 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358017341 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341 Building ZINC001358017341 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358017341 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 102) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H](c1ccccc1)c1ccc(Br)cc1F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001358017341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358017341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001358017341 none O=C(N[C@@H](c1ccccc1)c1ccc(Br)cc1F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 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] 0 hydrogens 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, 6, 6, 11, 11, 26, 26, 11, 26, 26, 11, 39, 39, 19, 39, 39, 39, 39, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 26, 26, 11, 26, 26, 39, 39, 39, 3, 3, 3, 3] 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]) total number of confs: 216 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 103) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H](c1ccccc1)c1ccc(Br)cc1F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001358017341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358017341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001358017341 none O=C(N[C@@H](c1ccccc1)c1ccc(Br)cc1F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 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] 0 hydrogens 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, 10, 10, 24, 24, 10, 24, 24, 10, 40, 40, 19, 40, 40, 40, 40, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 24, 24, 10, 24, 24, 40, 40, 40, 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]) total number of confs: 221 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358017341 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017341 Building ZINC001358017343 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358017343 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/104 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1ccccc1)c1ccc(Br)cc1F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001358017343.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358017343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001358017343 none O=C(N[C@H](c1ccccc1)c1ccc(Br)cc1F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 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] 0 hydrogens 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, 6, 6, 11, 11, 25, 25, 13, 25, 25, 11, 41, 41, 14, 41, 41, 41, 41, 1, 1, 1, 4, 4, 1, 2, 4, 4, 6, 25, 25, 25, 25, 25, 41, 41, 41, 4, 4, 4, 4] 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]) total number of confs: 235 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/105 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1ccccc1)c1ccc(Br)cc1F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001358017343.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358017343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001358017343 none O=C(N[C@H](c1ccccc1)c1ccc(Br)cc1F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 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] 0 hydrogens 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, 6, 6, 11, 11, 26, 26, 12, 26, 26, 11, 39, 39, 21, 39, 39, 39, 39, 1, 1, 1, 4, 4, 1, 1, 4, 4, 6, 26, 26, 14, 26, 26, 39, 39, 39, 4, 4, 4, 4] 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]) total number of confs: 215 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358017343 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343 Building ZINC001358017343 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358017343 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 104) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@H](c1ccccc1)c1ccc(Br)cc1F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001358017343.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358017343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001358017343 none O=C(N[C@H](c1ccccc1)c1ccc(Br)cc1F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 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] 0 hydrogens 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, 6, 6, 11, 11, 25, 25, 13, 25, 25, 11, 41, 41, 14, 41, 41, 41, 41, 1, 1, 1, 4, 4, 1, 2, 4, 4, 6, 25, 25, 25, 25, 25, 41, 41, 41, 4, 4, 4, 4] 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]) total number of confs: 235 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 105) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@H](c1ccccc1)c1ccc(Br)cc1F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001358017343.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358017343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001358017343 none O=C(N[C@H](c1ccccc1)c1ccc(Br)cc1F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 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] 0 hydrogens 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, 6, 6, 11, 11, 26, 26, 12, 26, 26, 11, 39, 39, 21, 39, 39, 39, 39, 1, 1, 1, 4, 4, 1, 1, 4, 4, 6, 26, 26, 14, 26, 26, 39, 39, 39, 4, 4, 4, 4] 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]) total number of confs: 215 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358017343 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358017343 Building ZINC001358038092 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358038092 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/106 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2cccc(Cl)c2)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358038092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358038092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC001358038092 none O=C(Nc1nnc(c2cccc(Cl)c2)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 12, 12, 12, 12, 29, 29, 21, 29, 29, 29, 12, 1, 1, 1, 11, 11, 11, 11, 11, 6, 29, 29, 29, 29, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/107 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2cccc(Cl)c2)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358038092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358038092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC001358038092 none O=C(Nc1nnc(c2cccc(Cl)c2)s1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 11, 11, 11, 11, 29, 29, 19, 29, 29, 29, 11, 1, 1, 1, 11, 11, 11, 11, 11, 6, 29, 29, 20, 29, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358038092 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092 Building ZINC001358038092 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358038092 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 106) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/106: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Nc1nnc(c2cccc(Cl)c2)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358038092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358038092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC001358038092 none O=C(Nc1nnc(c2cccc(Cl)c2)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 12, 12, 12, 12, 29, 29, 21, 29, 29, 29, 12, 1, 1, 1, 11, 11, 11, 11, 11, 6, 29, 29, 29, 29, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 107) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/107: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Nc1nnc(c2cccc(Cl)c2)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358038092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358038092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC001358038092 none O=C(Nc1nnc(c2cccc(Cl)c2)s1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 11, 11, 11, 11, 29, 29, 19, 29, 29, 29, 11, 1, 1, 1, 11, 11, 11, 11, 11, 6, 29, 29, 20, 29, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358038092 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358038092 Building ZINC001358041819 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358041819 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/108 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(c2cccs2)nc2ccccn21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358041819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358041819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001358041819 none O=C(Nc1c(c2cccs2)nc2ccccn21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 14, 8, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens 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, 12, 15, 15, 37, 37, 37, 37, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 12, 37, 37, 37, 15, 15, 15, 15, 7, 7] 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/109 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/109' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(c2cccs2)nc2ccccn21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358041819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358041819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001358041819 none O=C(Nc1c(c2cccs2)nc2ccccn21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 14, 8, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens 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, 11, 14, 14, 36, 36, 36, 36, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 7, 7, 7, 7, 7, 11, 36, 36, 36, 14, 14, 14, 14, 7, 7] 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358041819 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819 Building ZINC001358041819 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358041819 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 108) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1c(c2cccs2)nc2ccccn21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358041819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358041819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001358041819 none O=C(Nc1c(c2cccs2)nc2ccccn21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 14, 8, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens 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, 12, 15, 15, 37, 37, 37, 37, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 12, 37, 37, 37, 15, 15, 15, 15, 7, 7] 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 109) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1c(c2cccs2)nc2ccccn21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358041819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358041819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001358041819 none O=C(Nc1c(c2cccs2)nc2ccccn21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 14, 8, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens 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, 11, 14, 14, 36, 36, 36, 36, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 7, 7, 7, 7, 7, 11, 36, 36, 36, 14, 14, 14, 14, 7, 7] 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358041819 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358041819 Building ZINC001358042314 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358042314 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/110 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)Nc1cc(Cl)ccc1Cl) `ZINC001358042314.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358042314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358042314 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)Nc1cc(Cl)ccc1Cl 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.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 7, 7, 7, 7, 25, 25, 25, 47, 47, 47, 45, 47, 47, 47, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 25, 47, 45, 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]) total number of confs: 111 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/111 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)Nc1cc(Cl)ccc1Cl) `ZINC001358042314.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358042314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358042314 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)Nc1cc(Cl)ccc1Cl 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.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 47, 47, 47, 46, 47, 47, 47, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 27, 47, 46, 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]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358042314 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314 Building ZINC001358042314 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358042314 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 110) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/110: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1CCCC[C@@H]1C(=O)Nc1cc(Cl)ccc1Cl) `ZINC001358042314.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358042314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358042314 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)Nc1cc(Cl)ccc1Cl 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.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 7, 7, 7, 7, 25, 25, 25, 47, 47, 47, 45, 47, 47, 47, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 25, 47, 45, 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]) total number of confs: 111 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 111) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/111: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1CCCC[C@@H]1C(=O)Nc1cc(Cl)ccc1Cl) `ZINC001358042314.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358042314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358042314 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)Nc1cc(Cl)ccc1Cl 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.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 47, 47, 47, 46, 47, 47, 47, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 27, 47, 46, 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]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358042314 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042314 Building ZINC001358042315 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358042315 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/112 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)Nc1cc(Cl)ccc1Cl) `ZINC001358042315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358042315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358042315 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)Nc1cc(Cl)ccc1Cl 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.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 48, 48, 48, 47, 48, 48, 48, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 27, 48, 48, 48] 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: 114 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/113 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/113' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)Nc1cc(Cl)ccc1Cl) `ZINC001358042315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358042315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358042315 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)Nc1cc(Cl)ccc1Cl 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.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 8, 8, 8, 8, 27, 27, 27, 48, 48, 48, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 27, 48, 48, 48] 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: 110 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358042315 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315 Building ZINC001358042315 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358042315 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 112) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)Nc1cc(Cl)ccc1Cl) `ZINC001358042315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358042315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358042315 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)Nc1cc(Cl)ccc1Cl 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.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 48, 48, 48, 47, 48, 48, 48, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 27, 48, 48, 48] 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: 114 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 113) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)Nc1cc(Cl)ccc1Cl) `ZINC001358042315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358042315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358042315 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)Nc1cc(Cl)ccc1Cl 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.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 8, 8, 8, 8, 27, 27, 27, 48, 48, 48, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 27, 48, 48, 48] 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: 110 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358042315 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358042315 Building ZINC001358048881 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358048881 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/114 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(c2ccc3c(c2)CCO3)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358048881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358048881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358048881 none O=C(NCc1ccc(c2ccc3c(c2)CCO3)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 11, 19, 19, 15, 19, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 1, 1, 1, 2, 2, 2, 2, 2, 2, 11, 11, 19, 19, 50, 50, 50, 50, 50, 50, 50, 19, 19, 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/115 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/115' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(c2ccc3c(c2)CCO3)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358048881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358048881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358048881 none O=C(NCc1ccc(c2ccc3c(c2)CCO3)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 11, 20, 20, 12, 20, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 2, 2, 2, 2, 2, 2, 11, 11, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358048881 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881 Building ZINC001358048881 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358048881 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 114) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1ccc(c2ccc3c(c2)CCO3)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358048881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358048881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358048881 none O=C(NCc1ccc(c2ccc3c(c2)CCO3)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 11, 19, 19, 15, 19, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 1, 1, 1, 2, 2, 2, 2, 2, 2, 11, 11, 19, 19, 50, 50, 50, 50, 50, 50, 50, 19, 19, 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 115) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1ccc(c2ccc3c(c2)CCO3)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358048881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358048881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358048881 none O=C(NCc1ccc(c2ccc3c(c2)CCO3)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 11, 20, 20, 12, 20, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 2, 2, 2, 2, 2, 2, 11, 11, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358048881 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358048881 Building ZINC001358106336 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358106336 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/116 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cccc(C(F)(F)F)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358106336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358106336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001358106336 none O=C(NCC1(c2cccc(C(F)(F)F)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 13, 29, 41, 41, 29, 41, 41, 41, 41, 41, 41, 29, 29, 1, 1, 1, 7, 7, 7, 7, 7, 2, 13, 13, 41, 41, 29, 41, 29, 29, 29, 29, 7, 7] 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/117 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/117' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cccc(C(F)(F)F)c2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358106336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358106336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001358106336 none O=C(NCC1(c2cccc(C(F)(F)F)c2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 13, 31, 43, 43, 35, 43, 43, 43, 43, 43, 43, 31, 31, 1, 1, 1, 6, 6, 6, 6, 6, 2, 13, 13, 43, 43, 31, 43, 31, 31, 31, 31, 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]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358106336 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336 Building ZINC001358106336 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358106336 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 116) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCC1(c2cccc(C(F)(F)F)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358106336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358106336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001358106336 none O=C(NCC1(c2cccc(C(F)(F)F)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 13, 29, 41, 41, 29, 41, 41, 41, 41, 41, 41, 29, 29, 1, 1, 1, 7, 7, 7, 7, 7, 2, 13, 13, 41, 41, 29, 41, 29, 29, 29, 29, 7, 7] 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 117) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCC1(c2cccc(C(F)(F)F)c2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358106336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358106336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001358106336 none O=C(NCC1(c2cccc(C(F)(F)F)c2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 13, 31, 43, 43, 35, 43, 43, 43, 43, 43, 43, 31, 31, 1, 1, 1, 6, 6, 6, 6, 6, 2, 13, 13, 43, 43, 31, 43, 31, 31, 31, 31, 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]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358106336 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358106336 Building ZINC001358115758 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358115758 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/118 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CNC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001358115758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358115758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358115758 none CC(C)CNC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 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] 0 hydrogens 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, 50, 50, 31, 31, 8, 31, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 8, 8, 2, 2, 1, 2, 8] 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/119 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CNC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001358115758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358115758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358115758 none CC(C)CNC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 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] 0 hydrogens 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, 50, 50, 30, 30, 8, 30, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 8, 8, 2, 2, 1, 2, 8] 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]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358115758 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758 Building ZINC001358115758 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358115758 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 118) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)CNC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001358115758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358115758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358115758 none CC(C)CNC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 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] 0 hydrogens 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, 50, 50, 31, 31, 8, 31, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 8, 8, 2, 2, 1, 2, 8] 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 119) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)CNC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001358115758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358115758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358115758 none CC(C)CNC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 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] 0 hydrogens 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, 50, 50, 30, 30, 8, 30, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 8, 8, 2, 2, 1, 2, 8] 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]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358115758 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358115758 Building ZINC001358162123 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358162123 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/120 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(CN2C(=O)Cc3ccc(Cl)cc32)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001358162123.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358162123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001358162123 none O=C(Nc1ccc(CN2C(=O)Cc3ccc(Cl)cc32)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 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, 7, 7, 6, 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] 0 hydrogens need 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, 2, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 2, 5, 5, 25, 25, 37, 37, 37, 37, 37, 5, 5, 4, 4] 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/121 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/121' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(CN2C(=O)Cc3ccc(Cl)cc32)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001358162123.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358162123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001358162123 none O=C(Nc1ccc(CN2C(=O)Cc3ccc(Cl)cc32)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 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, 7, 7, 6, 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] 0 hydrogens need 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, 5, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 2, 5, 5, 25, 25, 37, 37, 37, 37, 37, 5, 5, 4, 4] 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358162123 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123 Building ZINC001358162123 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358162123 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 120) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1ccc(CN2C(=O)Cc3ccc(Cl)cc32)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001358162123.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358162123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001358162123 none O=C(Nc1ccc(CN2C(=O)Cc3ccc(Cl)cc32)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 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, 7, 7, 6, 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] 0 hydrogens need 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, 2, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 2, 5, 5, 25, 25, 37, 37, 37, 37, 37, 5, 5, 4, 4] 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 121) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1ccc(CN2C(=O)Cc3ccc(Cl)cc32)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001358162123.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358162123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001358162123 none O=C(Nc1ccc(CN2C(=O)Cc3ccc(Cl)cc32)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 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, 7, 7, 6, 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] 0 hydrogens need 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, 5, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 2, 5, 5, 25, 25, 37, 37, 37, 37, 37, 5, 5, 4, 4] 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358162123 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358162123 Building ZINC001358182065 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358182065 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/122 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1OC(F)F) `ZINC001358182065.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358182065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001358182065 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1OC(F)F 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', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 16, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 8, 23, 23, 23, 8, 23, 23, 23, 30, 39, 39, 8, 8, 8, 4, 7, 7, 23, 23, 23, 39] 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/123 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/123' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1OC(F)F) `ZINC001358182065.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358182065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001358182065 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1OC(F)F 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', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 16, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 6, 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] 0 hydrogens 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, 7, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 7, 22, 22, 22, 8, 22, 22, 22, 24, 36, 36, 7, 7, 7, 4, 8, 8, 22, 22, 22, 36] 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358182065 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065 Building ZINC001358182065 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358182065 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 122) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/122: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c1ccc(Br)s1)c1cc(Cl)ccc1OC(F)F) `ZINC001358182065.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358182065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001358182065 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1OC(F)F 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', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 16, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 8, 23, 23, 23, 8, 23, 23, 23, 30, 39, 39, 8, 8, 8, 4, 7, 7, 23, 23, 23, 39] 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 123) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/123: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c1ccc(Br)s1)c1cc(Cl)ccc1OC(F)F) `ZINC001358182065.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358182065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001358182065 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1OC(F)F 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', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 16, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 6, 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] 0 hydrogens 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, 7, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 7, 22, 22, 22, 8, 22, 22, 22, 24, 36, 36, 7, 7, 7, 4, 8, 8, 22, 22, 22, 36] 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358182065 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358182065 Building ZINC001358185634 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358185634 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/124 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/124' -> `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)(C)c1ccccc1) `ZINC001358185634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358185634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001358185634 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)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', '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'] dock atom type 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, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 1, 4, 4, 4, 8, 8, 8, 15, 15, 9, 15, 15, 2, 2, 2, 11, 11, 3, 11, 2, 2, 2, 4, 8, 8, 8, 8, 8, 8, 15, 15, 11, 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]) total number of confs: 84 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/125 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/125' -> `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)(C)c1ccccc1) `ZINC001358185634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358185634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001358185634 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)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', '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'] dock atom type 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, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 1, 4, 4, 4, 8, 8, 8, 15, 15, 10, 15, 15, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 4, 8, 8, 8, 8, 8, 8, 15, 15, 11, 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]) total number of confs: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358185634 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634 Building ZINC001358185634 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358185634 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 124) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)c1ccccc1) `ZINC001358185634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358185634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001358185634 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)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', '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'] dock atom type 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, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 1, 4, 4, 4, 8, 8, 8, 15, 15, 9, 15, 15, 2, 2, 2, 11, 11, 3, 11, 2, 2, 2, 4, 8, 8, 8, 8, 8, 8, 15, 15, 11, 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]) total number of confs: 84 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 125) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)c1ccccc1) `ZINC001358185634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358185634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001358185634 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)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', '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'] dock atom type 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, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 1, 4, 4, 4, 8, 8, 8, 15, 15, 10, 15, 15, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 4, 8, 8, 8, 8, 8, 8, 15, 15, 11, 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]) total number of confs: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358185634 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358185634 Building ZINC001358197408 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358197408 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/126 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/126' -> `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)c1cc(C)cc(C)c1) `ZINC001358197408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358197408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001358197408 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1cc(C)cc(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.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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'] dock atom type 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, 5, 1, 1, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 10, 10, 10, 5, 10, 10, 10, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 5, 5, 5, 10, 10, 10, 10, 7, 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]) total number of confs: 68 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/127 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/127' -> `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)c1cc(C)cc(C)c1) `ZINC001358197408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358197408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001358197408 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1cc(C)cc(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.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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'] dock atom type 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, 5, 1, 1, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 10, 10, 10, 8, 10, 10, 10, 3, 3, 3, 13, 13, 5, 13, 3, 3, 3, 5, 5, 5, 10, 10, 10, 10, 8, 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]) total number of confs: 63 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358197408 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408 Building ZINC001358197408 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358197408 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 126) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1cc(C)cc(C)c1) `ZINC001358197408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358197408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001358197408 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1cc(C)cc(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.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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'] dock atom type 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, 5, 1, 1, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 10, 10, 10, 5, 10, 10, 10, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 5, 5, 5, 10, 10, 10, 10, 7, 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]) total number of confs: 68 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 127) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1cc(C)cc(C)c1) `ZINC001358197408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358197408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001358197408 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1cc(C)cc(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.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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'] dock atom type 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, 5, 1, 1, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 10, 10, 10, 8, 10, 10, 10, 3, 3, 3, 13, 13, 5, 13, 3, 3, 3, 5, 5, 5, 10, 10, 10, 10, 8, 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]) total number of confs: 63 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358197408 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358197408 Building ZINC001358199869 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358199869 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/128 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(Cc3ccc(c4cccc(Cl)c4)s3)CC2)c1) `ZINC001358199869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358199869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358199869 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(Cc3ccc(c4cccc(Cl)c4)s3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 7, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 9, 3, 3, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 7, 7, 9, 9, 30, 30, 30, 30, 3, 3, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/129 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/129' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(Cc3ccc(c4cccc(Cl)c4)s3)CC2)c1) `ZINC001358199869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358199869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358199869 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(Cc3ccc(c4cccc(Cl)c4)s3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 6, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 9, 3, 3, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 6, 6, 9, 9, 29, 29, 29, 29, 3, 3, 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358199869 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869 Building ZINC001358199869 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358199869 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 128) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(Cc3ccc(c4cccc(Cl)c4)s3)CC2)c1) `ZINC001358199869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358199869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358199869 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(Cc3ccc(c4cccc(Cl)c4)s3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 7, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 9, 3, 3, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 7, 7, 9, 9, 30, 30, 30, 30, 3, 3, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 129) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(Cc3ccc(c4cccc(Cl)c4)s3)CC2)c1) `ZINC001358199869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358199869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358199869 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(Cc3ccc(c4cccc(Cl)c4)s3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 6, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 9, 3, 3, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 6, 6, 9, 9, 29, 29, 29, 29, 3, 3, 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358199869 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358199869 Building ZINC001358206394 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358206394 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/130 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(c1nnc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1) `ZINC001358206394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358206394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001358206394 none CC(C)(c1nnc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.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'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 1, 1, 1, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 30, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 4, 30, 39, 39, 34, 39, 39, 30, 30, 30, 30, 30, 30, 2, 7, 7, 39, 39, 38, 39, 39] 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/131 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/131' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(c1nnc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1) `ZINC001358206394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358206394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001358206394 none CC(C)(c1nnc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.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'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 1, 1, 1, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 30, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 4, 30, 39, 39, 35, 39, 39, 30, 30, 30, 30, 30, 30, 2, 7, 7, 39, 39, 39, 39, 39] 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358206394 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394 Building ZINC001358206394 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358206394 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 130) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)(c1nnc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1) `ZINC001358206394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358206394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001358206394 none CC(C)(c1nnc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.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'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 1, 1, 1, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 30, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 4, 30, 39, 39, 34, 39, 39, 30, 30, 30, 30, 30, 30, 2, 7, 7, 39, 39, 38, 39, 39] 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 131) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)(c1nnc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1) `ZINC001358206394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358206394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001358206394 none CC(C)(c1nnc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.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'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 1, 1, 1, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 30, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 4, 30, 39, 39, 35, 39, 39, 30, 30, 30, 30, 30, 30, 2, 7, 7, 39, 39, 39, 39, 39] 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358206394 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358206394 Building ZINC001358224298 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358224298 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/132 `/scratch/xiaobo/182395/xbh-8058088.34/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)NCc1ccc(C)cc1C) `ZINC001358224298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358224298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001358224298 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', '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'] dock atom type 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, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 12, 12, 8, 8, 12, 8, 12, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 8, 8, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/133 `/scratch/xiaobo/182395/xbh-8058088.34/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)NCc1ccc(C)cc1C) `ZINC001358224298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358224298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001358224298 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', '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'] dock atom type 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, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 14, 14, 8, 8, 14, 10, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358224298 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298 Building ZINC001358224298 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358224298 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 132) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)NCc1ccc(C)cc1C) `ZINC001358224298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358224298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001358224298 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', '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'] dock atom type 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, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 12, 12, 8, 8, 12, 8, 12, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 8, 8, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 133) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)NCc1ccc(C)cc1C) `ZINC001358224298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358224298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001358224298 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', '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'] dock atom type 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, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 14, 14, 8, 8, 14, 10, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358224298 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358224298 Building ZINC001358230428 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358230428 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/134 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/134' -> `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)NCc1c(C)cc(C)cc1C) `ZINC001358230428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358230428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001358230428 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1c(C)cc(C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.3', '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'] dock atom type 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, 5, 1, 1, 5, 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, 7, 7] dock 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] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 4, 10, 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, 55]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/135 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/135' -> `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)NCc1c(C)cc(C)cc1C) `ZINC001358230428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358230428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001358230428 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1c(C)cc(C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.3', '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'] dock atom type 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, 5, 1, 1, 5, 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, 7, 7] dock 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] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 14, 14, 4, 14, 3, 3, 3, 3, 9, 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, 55]) total number of confs: 67 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358230428 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428 Building ZINC001358230428 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358230428 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 134) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1c(C)cc(C)cc1C) `ZINC001358230428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358230428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001358230428 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1c(C)cc(C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.3', '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'] dock atom type 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, 5, 1, 1, 5, 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, 7, 7] dock 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] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 4, 10, 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, 55]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 135) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1c(C)cc(C)cc1C) `ZINC001358230428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358230428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001358230428 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1c(C)cc(C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.3', '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'] dock atom type 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, 5, 1, 1, 5, 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, 7, 7] dock 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] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 14, 14, 4, 14, 3, 3, 3, 3, 9, 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, 55]) total number of confs: 67 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358230428 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358230428 Building ZINC001358258907 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358258907 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/136 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001358258907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358258907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001358258907 none O=C(NCc1ccccc1)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)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.ar', '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', 'Cl', '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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens 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, 9, 15, 15, 44, 48, 48, 44, 48, 48, 9, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 15, 44, 44, 48, 48, 44, 48, 48, 9, 9, 9, 2, 3, 1, 3, 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/137 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1)c1cccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001358258907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358258907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001358258907 none O=C(NCc1ccccc1)c1cccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)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.ar', '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', 'Cl', '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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens 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, 9, 15, 15, 43, 47, 47, 43, 47, 47, 9, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 15, 43, 43, 47, 47, 43, 47, 47, 9, 9, 9, 2, 3, 1, 3, 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358258907 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907 Building ZINC001358258907 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358258907 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 136) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(NCc1ccccc1)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001358258907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358258907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001358258907 none O=C(NCc1ccccc1)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)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.ar', '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', 'Cl', '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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens 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, 9, 15, 15, 44, 48, 48, 44, 48, 48, 9, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 15, 44, 44, 48, 48, 44, 48, 48, 9, 9, 9, 2, 3, 1, 3, 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 137) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(NCc1ccccc1)c1cccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001358258907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358258907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001358258907 none O=C(NCc1ccccc1)c1cccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)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.ar', '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', 'Cl', '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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens 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, 9, 15, 15, 43, 47, 47, 43, 47, 47, 9, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 15, 43, 43, 47, 47, 43, 47, 47, 9, 9, 9, 2, 3, 1, 3, 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358258907 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358258907 Building ZINC001358285890 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358285890 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/138 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(c4cc(F)ccc4F)[nH]c3c2)cc1Cl) `ZINC001358285890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358285890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001358285890 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(c4cc(F)ccc4F)[nH]c3c2)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.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 6, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 6, 6, 6, 11, 11, 11, 6, 6, 2, 9, 9, 26, 25, 26, 9, 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, 40, 41, 42, 43, 44]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/139 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/139' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(c4cc(F)ccc4F)[nH]c3c2)cc1Cl) `ZINC001358285890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358285890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001358285890 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(c4cc(F)ccc4F)[nH]c3c2)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.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 6, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 6, 6, 6, 11, 11, 11, 6, 6, 2, 9, 9, 26, 26, 26, 9, 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, 40, 41, 42, 43, 44]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358285890 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890 Building ZINC001358285890 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358285890 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 138) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(c4cc(F)ccc4F)[nH]c3c2)cc1Cl) `ZINC001358285890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358285890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001358285890 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(c4cc(F)ccc4F)[nH]c3c2)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.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 6, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 6, 6, 6, 11, 11, 11, 6, 6, 2, 9, 9, 26, 25, 26, 9, 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, 40, 41, 42, 43, 44]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 139) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(c4cc(F)ccc4F)[nH]c3c2)cc1Cl) `ZINC001358285890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358285890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001358285890 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(c4cc(F)ccc4F)[nH]c3c2)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.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 6, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 6, 6, 6, 11, 11, 11, 6, 6, 2, 9, 9, 26, 26, 26, 9, 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, 40, 41, 42, 43, 44]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358285890 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358285890 Building ZINC001358291316 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358291316 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/140 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccc3c(c2)OCO3)C2CCCCC2)cc1Cl) `ZINC001358291316.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358291316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358291316 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccc3c(c2)OCO3)C2CCCCC2)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', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 5, 1, 1, 1, 1, 1, 1, 12, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 17, 17, 17, 17, 17, 17, 17, 17, 3, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 6, 6, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/141 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/141' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccc3c(c2)OCO3)C2CCCCC2)cc1Cl) `ZINC001358291316.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358291316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358291316 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccc3c(c2)OCO3)C2CCCCC2)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', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 5, 1, 1, 1, 1, 1, 1, 12, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 17, 17, 17, 17, 17, 17, 17, 17, 3, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 6, 6, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358291316 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316 Building ZINC001358291316 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358291316 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 140) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccc3c(c2)OCO3)C2CCCCC2)cc1Cl) `ZINC001358291316.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358291316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358291316 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccc3c(c2)OCO3)C2CCCCC2)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', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 5, 1, 1, 1, 1, 1, 1, 12, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 17, 17, 17, 17, 17, 17, 17, 17, 3, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 6, 6, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 141) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccc3c(c2)OCO3)C2CCCCC2)cc1Cl) `ZINC001358291316.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358291316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358291316 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccc3c(c2)OCO3)C2CCCCC2)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', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 5, 1, 1, 1, 1, 1, 1, 12, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 17, 17, 17, 17, 17, 17, 17, 17, 3, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 6, 6, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358291316 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358291316 Building ZINC001358301130 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358301130 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/142 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/142' -> `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(COc2ccccc2)c1) `ZINC001358301130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358301130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001358301130 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(COc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'O.3', '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'] 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, 12, 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, 7, 7, 7] dock 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 2, 2, 9, 9, 2, 9, 9, 38, 38, 38, 38, 38, 38, 38, 9, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 9, 9, 2, 38, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 153 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/143 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/143' -> `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(COc2ccccc2)c1) `ZINC001358301130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358301130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001358301130 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(COc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'O.3', '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'] 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, 12, 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, 7, 7, 7] dock 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 6, 10, 10, 41, 41, 41, 41, 41, 41, 41, 10, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 10, 10, 9, 41, 41, 41, 41, 41, 41, 41, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358301130 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130 Building ZINC001358301130 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358301130 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 142) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(COc2ccccc2)c1) `ZINC001358301130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358301130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001358301130 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(COc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'O.3', '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'] 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, 12, 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, 7, 7, 7] dock 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 2, 2, 9, 9, 2, 9, 9, 38, 38, 38, 38, 38, 38, 38, 9, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 9, 9, 2, 38, 38, 38, 38, 38, 38, 38, 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]) total number of confs: 153 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 143) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(COc2ccccc2)c1) `ZINC001358301130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358301130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001358301130 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(COc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'O.3', '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'] 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, 12, 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, 7, 7, 7] dock 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 6, 10, 10, 41, 41, 41, 41, 41, 41, 41, 10, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 10, 10, 9, 41, 41, 41, 41, 41, 41, 41, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358301130 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358301130 Building ZINC001358357475 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358357475 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/144 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(N2C(=O)c3ccccc3C2=O)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001358357475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358357475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001358357475 none O=C(Nc1cccc(N2C(=O)c3ccccc3C2=O)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.ar', 'C.2', 'O.2', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 20, 20, 20, 37, 37, 37, 37, 20, 3, 1, 3] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/145 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/145' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(N2C(=O)c3ccccc3C2=O)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001358357475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358357475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001358357475 none O=C(Nc1cccc(N2C(=O)c3ccccc3C2=O)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.ar', 'C.2', 'O.2', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 20, 20, 20, 37, 37, 37, 37, 20, 3, 1, 3] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358357475 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475 Building ZINC001358357475 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358357475 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 144) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cccc(N2C(=O)c3ccccc3C2=O)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001358357475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358357475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001358357475 none O=C(Nc1cccc(N2C(=O)c3ccccc3C2=O)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.ar', 'C.2', 'O.2', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 20, 20, 20, 37, 37, 37, 37, 20, 3, 1, 3] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 145) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cccc(N2C(=O)c3ccccc3C2=O)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001358357475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358357475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001358357475 none O=C(Nc1cccc(N2C(=O)c3ccccc3C2=O)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.ar', 'C.2', 'O.2', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 20, 20, 20, 37, 37, 37, 37, 20, 3, 1, 3] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358357475 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358357475 Building ZINC001358369729 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358369729 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/146 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1cc(C(F)(F)F)ccc1NC(=O)OC(C)(C)C) `ZINC001358369729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358369729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001358369729 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1cc(C(F)(F)F)ccc1NC(=O)OC(C)(C)C 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', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 6, 13, 13, 13, 22, 32, 32, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 4, 13, 13, 13, 22, 49, 49, 49, 49, 49, 49, 49, 49, 49] 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/147 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1cc(C(F)(F)F)ccc1NC(=O)OC(C)(C)C) `ZINC001358369729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358369729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001358369729 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1cc(C(F)(F)F)ccc1NC(=O)OC(C)(C)C 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', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 6, 13, 13, 13, 21, 31, 31, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 4, 13, 13, 13, 21, 49, 49, 49, 49, 49, 49, 49, 49, 49] 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358369729 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729 Building ZINC001358369729 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358369729 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 146) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1cc(C(F)(F)F)ccc1NC(=O)OC(C)(C)C) `ZINC001358369729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358369729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001358369729 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1cc(C(F)(F)F)ccc1NC(=O)OC(C)(C)C 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', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 6, 13, 13, 13, 22, 32, 32, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 4, 13, 13, 13, 22, 49, 49, 49, 49, 49, 49, 49, 49, 49] 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 147) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1cc(C(F)(F)F)ccc1NC(=O)OC(C)(C)C) `ZINC001358369729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358369729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001358369729 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1cc(C(F)(F)F)ccc1NC(=O)OC(C)(C)C 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', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 6, 13, 13, 13, 21, 31, 31, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 4, 13, 13, 13, 21, 49, 49, 49, 49, 49, 49, 49, 49, 49] 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358369729 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358369729 Building ZINC001358376918 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358376918 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/148 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1CN(Cc1cccnc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358376918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358376918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358376918 none Cc1ccccc1CN(Cc1cccnc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 5, 8, 5, 1, 1, 1, 1, 8, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 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: [12, 12, 12, 10, 12, 12, 10, 6, 3, 6, 10, 17, 17, 17, 17, 17, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 10, 10, 10, 10, 17, 17, 17, 17, 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/149 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/149' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1CN(Cc1cccnc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358376918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358376918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358376918 none Cc1ccccc1CN(Cc1cccnc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 5, 8, 5, 1, 1, 1, 1, 8, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 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: [12, 12, 12, 10, 12, 12, 10, 6, 3, 6, 11, 18, 18, 18, 18, 18, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 12, 12, 10, 12, 12, 10, 10, 11, 11, 18, 18, 18, 18, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358376918 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918 Building ZINC001358376918 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358376918 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 148) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccccc1CN(Cc1cccnc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358376918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358376918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358376918 none Cc1ccccc1CN(Cc1cccnc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 5, 8, 5, 1, 1, 1, 1, 8, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 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: [12, 12, 12, 10, 12, 12, 10, 6, 3, 6, 10, 17, 17, 17, 17, 17, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 10, 10, 10, 10, 17, 17, 17, 17, 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 149) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccccc1CN(Cc1cccnc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358376918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358376918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001358376918 none Cc1ccccc1CN(Cc1cccnc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 5, 8, 5, 1, 1, 1, 1, 8, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 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: [12, 12, 12, 10, 12, 12, 10, 6, 3, 6, 11, 18, 18, 18, 18, 18, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 12, 12, 10, 12, 12, 10, 10, 11, 11, 18, 18, 18, 18, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358376918 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358376918 Building ZINC001358399129 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358399129 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/150 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](Cc1ccc(Cl)cc1)c1ccccn1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358399129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358399129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001358399129 none O=C(N[C@@H](Cc1ccc(Cl)cc1)c1ccccn1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 20, 20, 20, 20, 20, 20, 20, 9, 22, 22, 22, 22, 22, 1, 1, 1, 9, 9, 9, 9, 9, 5, 20, 20, 20, 20, 20, 20, 22, 22, 22, 22, 9, 9] 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/151 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/151' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](Cc1ccc(Cl)cc1)c1ccccn1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358399129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358399129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001358399129 none O=C(N[C@@H](Cc1ccc(Cl)cc1)c1ccccn1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 21, 21, 21, 21, 21, 21, 21, 9, 21, 21, 21, 21, 21, 1, 1, 1, 9, 9, 9, 9, 9, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 9] 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358399129 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129 Building ZINC001358399129 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358399129 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 150) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H](Cc1ccc(Cl)cc1)c1ccccn1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358399129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358399129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001358399129 none O=C(N[C@@H](Cc1ccc(Cl)cc1)c1ccccn1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 20, 20, 20, 20, 20, 20, 20, 9, 22, 22, 22, 22, 22, 1, 1, 1, 9, 9, 9, 9, 9, 5, 20, 20, 20, 20, 20, 20, 22, 22, 22, 22, 9, 9] 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 151) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H](Cc1ccc(Cl)cc1)c1ccccn1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358399129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358399129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001358399129 none O=C(N[C@@H](Cc1ccc(Cl)cc1)c1ccccn1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 21, 21, 21, 21, 21, 21, 21, 9, 21, 21, 21, 21, 21, 1, 1, 1, 9, 9, 9, 9, 9, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 9] 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358399129 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399129 Building ZINC001358399139 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358399139 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/152 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](Cc1ccc(Cl)cc1)c1ccccn1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358399139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358399139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001358399139 none O=C(N[C@H](Cc1ccc(Cl)cc1)c1ccccn1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 21, 21, 21, 21, 21, 21, 21, 9, 21, 21, 21, 21, 21, 1, 1, 1, 9, 9, 9, 9, 9, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 9] 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/153 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/153' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](Cc1ccc(Cl)cc1)c1ccccn1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358399139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358399139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001358399139 none O=C(N[C@H](Cc1ccc(Cl)cc1)c1ccccn1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 21, 21, 21, 21, 21, 21, 21, 9, 22, 22, 22, 22, 22, 1, 1, 1, 9, 9, 9, 9, 9, 5, 21, 21, 21, 21, 21, 21, 22, 22, 22, 22, 9, 9] 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358399139 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139 Building ZINC001358399139 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358399139 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 152) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/152: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](Cc1ccc(Cl)cc1)c1ccccn1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358399139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358399139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001358399139 none O=C(N[C@H](Cc1ccc(Cl)cc1)c1ccccn1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 21, 21, 21, 21, 21, 21, 21, 9, 21, 21, 21, 21, 21, 1, 1, 1, 9, 9, 9, 9, 9, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 9] 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 153) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/153: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](Cc1ccc(Cl)cc1)c1ccccn1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358399139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358399139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001358399139 none O=C(N[C@H](Cc1ccc(Cl)cc1)c1ccccn1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 21, 21, 21, 21, 21, 21, 21, 9, 22, 22, 22, 22, 22, 1, 1, 1, 9, 9, 9, 9, 9, 5, 21, 21, 21, 21, 21, 21, 22, 22, 22, 22, 9, 9] 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358399139 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358399139 Building ZINC001358409276 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358409276 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/154 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001358409276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358409276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001358409276 none CC[C@@H](Cc1ccccc1)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', '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', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 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, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 4, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 1, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3] 50 rigid atoms, others: [2, 11, 12, 45, 14, 13, 16, 15] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 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: 89 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/155 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/155' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001358409276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358409276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001358409276 none CC[C@@H](Cc1ccccc1)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', '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', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 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, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 2, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3] 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]) total number of confs: 88 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358409276 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276 Building ZINC001358409276 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358409276 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 154) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC[C@@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001358409276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358409276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001358409276 none CC[C@@H](Cc1ccccc1)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', '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', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 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, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 4, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 1, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3] 50 rigid atoms, others: [2, 11, 12, 45, 14, 13, 16, 15] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 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: 89 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 155) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC[C@@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001358409276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358409276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001358409276 none CC[C@@H](Cc1ccccc1)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', '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', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 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, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 2, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3] 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]) total number of confs: 88 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358409276 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409276 Building ZINC001358409278 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358409278 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/156 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001358409278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358409278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001358409278 none CC[C@H](Cc1ccccc1)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', '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', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 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, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 4, 1, 4, 4, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 50 rigid atoms, others: [2, 11, 12, 45, 14, 13, 16, 15] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 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: 74 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/157 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/157' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001358409278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358409278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001358409278 none CC[C@H](Cc1ccccc1)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', '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', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 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, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 4, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 4, 16, 16, 16, 16, 16, 16, 4, 4, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 1, 4, 4, 4, 16, 16, 8, 16, 4, 4, 4] 50 rigid atoms, others: [2, 11, 12, 45, 14, 13, 16, 15] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 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: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358409278 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278 Building ZINC001358409278 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358409278 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 156) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/156: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001358409278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358409278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001358409278 none CC[C@H](Cc1ccccc1)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', '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', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 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, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 4, 1, 4, 4, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 50 rigid atoms, others: [2, 11, 12, 45, 14, 13, 16, 15] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 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: 74 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 157) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/157: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001358409278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358409278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001358409278 none CC[C@H](Cc1ccccc1)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', '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', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 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, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 4, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 4, 16, 16, 16, 16, 16, 16, 4, 4, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 1, 4, 4, 4, 16, 16, 8, 16, 4, 4, 4] 50 rigid atoms, others: [2, 11, 12, 45, 14, 13, 16, 15] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 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: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358409278 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358409278 Building ZINC001358464853 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358464853 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/158 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1) `ZINC001358464853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358464853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001358464853 none CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 9, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 15, 50, 50, 31, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 9, 9, 2, 2, 2, 50, 50, 49, 50] 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]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/159 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/159' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1) `ZINC001358464853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358464853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001358464853 none CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 9, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 15, 50, 50, 22, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 9, 9, 2, 2, 2, 50, 50, 22, 50] 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]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358464853 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853 Building ZINC001358464853 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358464853 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 158) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1) `ZINC001358464853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358464853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001358464853 none CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 9, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 15, 50, 50, 31, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 9, 9, 2, 2, 2, 50, 50, 49, 50] 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]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 159) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1) `ZINC001358464853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358464853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001358464853 none CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 9, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 15, 50, 50, 22, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 9, 9, 2, 2, 2, 50, 50, 22, 50] 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]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358464853 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358464853 Building ZINC001358493205 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358493205 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/160 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(OCc2ccccc2F)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358493205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358493205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001358493205 none O=C(NCc1ccc(OCc2ccccc2F)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', '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', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 3, 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] 0 hydrogens need 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, 17, 17, 9, 9, 27, 27, 50, 50, 27, 50, 50, 50, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 17, 17, 27, 27, 50, 50, 50, 50, 17, 17, 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]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/161 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/161' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(OCc2ccccc2F)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358493205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358493205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001358493205 none O=C(NCc1ccc(OCc2ccccc2F)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', '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', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 3, 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] 0 hydrogens need 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, 16, 16, 15, 16, 27, 27, 50, 50, 27, 50, 50, 50, 16, 16, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 16, 16, 27, 27, 50, 50, 50, 50, 16, 16, 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]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358493205 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205 Building ZINC001358493205 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358493205 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 160) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1ccc(OCc2ccccc2F)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358493205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358493205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001358493205 none O=C(NCc1ccc(OCc2ccccc2F)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', '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', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 3, 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] 0 hydrogens need 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, 17, 17, 9, 9, 27, 27, 50, 50, 27, 50, 50, 50, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 17, 17, 27, 27, 50, 50, 50, 50, 17, 17, 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]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 161) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1ccc(OCc2ccccc2F)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001358493205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358493205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001358493205 none O=C(NCc1ccc(OCc2ccccc2F)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', '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', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 3, 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] 0 hydrogens need 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, 16, 16, 15, 16, 27, 27, 50, 50, 27, 50, 50, 50, 16, 16, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 16, 16, 27, 27, 50, 50, 50, 50, 16, 16, 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]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001358493205 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001358493205 Building ZINC000605443541 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605443541 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/162 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/162' -> `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(C2CCCC2)[nH]n1) `ZINC000605443541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605443541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000605443541 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(C2CCCC2)[nH]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.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 6, 8, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 6, 12, 12, 12, 12, 5, 5, 5, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 5, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/163 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/163' -> `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(C2CCCC2)[nH]n1) `ZINC000605443541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605443541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000605443541 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(C2CCCC2)[nH]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.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 6, 8, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 6, 12, 12, 12, 12, 5, 5, 5, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 5, 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC000605443541 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541 Building ZINC000605443541 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000605443541 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 162) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(C2CCCC2)[nH]n1) `ZINC000605443541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000605443541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000605443541 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(C2CCCC2)[nH]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.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 6, 8, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 6, 12, 12, 12, 12, 5, 5, 5, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 5, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 163) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(C2CCCC2)[nH]n1) `ZINC000605443541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000605443541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000605443541 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(C2CCCC2)[nH]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.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 6, 8, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 6, 12, 12, 12, 12, 5, 5, 5, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 5, 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC000605443541 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000605443541 Building ZINC000608468552 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608468552 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/164 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/164' -> `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)Nc1n[nH]c(C)c1c1cccc(Cl)c1) `ZINC000608468552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608468552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000608468552 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1n[nH]c(C)c1c1cccc(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.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 8, 6, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 8, 8, 8, 8, 32, 32, 32, 32, 32, 32, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 3, 8, 8, 8, 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/165 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/165' -> `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)Nc1n[nH]c(C)c1c1cccc(Cl)c1) `ZINC000608468552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608468552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000608468552 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1n[nH]c(C)c1c1cccc(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.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 8, 6, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 8, 8, 8, 8, 31, 31, 31, 31, 31, 31, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 8, 8, 8, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC000608468552 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552 Building ZINC000608468552 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608468552 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 164) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1n[nH]c(C)c1c1cccc(Cl)c1) `ZINC000608468552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608468552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000608468552 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1n[nH]c(C)c1c1cccc(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.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 8, 6, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 8, 8, 8, 8, 32, 32, 32, 32, 32, 32, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 3, 8, 8, 8, 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 165) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1n[nH]c(C)c1c1cccc(Cl)c1) `ZINC000608468552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608468552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000608468552 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1n[nH]c(C)c1c1cccc(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.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 8, 6, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 8, 8, 8, 8, 31, 31, 31, 31, 31, 31, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 8, 8, 8, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC000608468552 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000608468552 Building ZINC000520728762 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000520728762 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/166 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](c1nnc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)s1)c1ccccc1) `ZINC000520728762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000520728762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000520728762 none CC[C@H](c1nnc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', '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', 'S.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, 5, 5, 7, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 14, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 16, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 16, 24, 24, 16, 24, 24, 24, 24, 24, 24, 24, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 24, 24, 16, 24, 24] 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: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/167 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/167' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](c1nnc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)s1)c1ccccc1) `ZINC000520728762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000520728762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000520728762 none CC[C@H](c1nnc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', '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', 'S.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, 5, 5, 7, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 14, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 4, 14, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 4, 14, 22, 22, 14, 22, 22, 24, 24, 24, 24, 24, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 22, 22, 14, 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC000520728762 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762 Building ZINC000520728762 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000520728762 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 166) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](c1nnc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)s1)c1ccccc1) `ZINC000520728762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000520728762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000520728762 none CC[C@H](c1nnc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', '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', 'S.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, 5, 5, 7, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 14, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 16, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 16, 24, 24, 16, 24, 24, 24, 24, 24, 24, 24, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 24, 24, 16, 24, 24] 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: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 167) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](c1nnc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)s1)c1ccccc1) `ZINC000520728762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000520728762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000520728762 none CC[C@H](c1nnc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', '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', 'S.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, 5, 5, 7, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 14, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 4, 14, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 4, 14, 22, 22, 14, 22, 22, 24, 24, 24, 24, 24, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 22, 22, 14, 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC000520728762 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728762 Building ZINC000520728763 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000520728763 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/168 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](c1nnc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)s1)c1ccccc1) `ZINC000520728763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000520728763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000520728763 none CC[C@@H](c1nnc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', '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', 'S.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, 5, 5, 7, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 14, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 4, 14, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 4, 14, 23, 23, 14, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 23, 23, 14, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/169 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/169' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](c1nnc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)s1)c1ccccc1) `ZINC000520728763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000520728763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000520728763 none CC[C@@H](c1nnc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', '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', 'S.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, 5, 5, 7, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 14, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 4, 15, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 15, 24, 24, 15, 24, 24, 23, 23, 23, 23, 23, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 24, 24, 15, 24, 24] 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: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC000520728763 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763 Building ZINC000520728763 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000520728763 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 168) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC[C@@H](c1nnc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)s1)c1ccccc1) `ZINC000520728763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000520728763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000520728763 none CC[C@@H](c1nnc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', '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', 'S.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, 5, 5, 7, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 14, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 4, 14, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 4, 14, 23, 23, 14, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 23, 23, 14, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 169) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC[C@@H](c1nnc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)s1)c1ccccc1) `ZINC000520728763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000520728763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000520728763 none CC[C@@H](c1nnc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', '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', 'S.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, 5, 5, 7, 1, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 14, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 4, 15, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 15, 24, 24, 15, 24, 24, 23, 23, 23, 23, 23, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 24, 24, 15, 24, 24] 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: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC000520728763 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000520728763 Building ZINC000617357549 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000617357549 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/170 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/170' -> `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)Nc1cc(c2cc(C)c(C)cc2C)[nH]n1) `ZINC000617357549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000617357549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000617357549 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(c2cc(C)c(C)cc2C)[nH]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.ar', 'C.2', 'C.3', '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.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'H', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 5, 8, 6, 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] dock 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 7, 7, 7, 32, 32, 32, 7, 13, 32, 32, 32, 7, 7, 7, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 3, 7, 32, 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]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/171 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/171' -> `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)Nc1cc(c2cc(C)c(C)cc2C)[nH]n1) `ZINC000617357549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000617357549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000617357549 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2cc(C)c(C)cc2C)[nH]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.ar', 'C.2', 'C.3', '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.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'H', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 5, 8, 6, 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] dock 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 33, 33, 33, 7, 8, 33, 33, 33, 7, 7, 7, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 3, 7, 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC000617357549 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549 Building ZINC000617357549 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000617357549 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 170) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(c2cc(C)c(C)cc2C)[nH]n1) `ZINC000617357549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000617357549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000617357549 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(c2cc(C)c(C)cc2C)[nH]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.ar', 'C.2', 'C.3', '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.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'H', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 5, 8, 6, 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] dock 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 7, 7, 7, 32, 32, 32, 7, 13, 32, 32, 32, 7, 7, 7, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 3, 7, 32, 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]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 171) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2cc(C)c(C)cc2C)[nH]n1) `ZINC000617357549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000617357549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000617357549 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2cc(C)c(C)cc2C)[nH]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.ar', 'C.2', 'C.3', '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.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'H', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 5, 8, 6, 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] dock 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 33, 33, 33, 7, 8, 33, 33, 33, 7, 7, 7, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 3, 7, 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC000617357549 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000617357549 Building ZINC000538464028 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000538464028 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/172 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)n1nc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C) `ZINC000538464028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000538464028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000538464028 none CC[C@@H](C)n1nc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', '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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 5, 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] 0 hydrogens 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, 13, 5, 13, 13, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 5, 5, 5, 15, 15, 15, 15, 15, 13, 13, 13, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/173 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/173' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)n1nc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C) `ZINC000538464028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000538464028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000538464028 none CC[C@@H](C)n1nc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', '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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 5, 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] 0 hydrogens 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, 12, 5, 12, 12, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 5, 5, 5, 15, 15, 15, 15, 15, 12, 12, 12, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC000538464028 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028 Building ZINC000538464028 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000538464028 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 172) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC[C@@H](C)n1nc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C) `ZINC000538464028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000538464028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000538464028 none CC[C@@H](C)n1nc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', '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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 5, 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] 0 hydrogens 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, 13, 5, 13, 13, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 5, 5, 5, 15, 15, 15, 15, 15, 13, 13, 13, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 173) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC[C@@H](C)n1nc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C) `ZINC000538464028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000538464028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000538464028 none CC[C@@H](C)n1nc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', '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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 5, 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] 0 hydrogens 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, 12, 5, 12, 12, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 5, 5, 5, 15, 15, 15, 15, 15, 12, 12, 12, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC000538464028 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464028 Building ZINC000538464030 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000538464030 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/174 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)n1nc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C) `ZINC000538464030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000538464030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000538464030 none CC[C@H](C)n1nc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', '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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 5, 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] 0 hydrogens 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, 11, 5, 11, 11, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 5, 5, 5, 13, 13, 13, 13, 13, 11, 11, 11, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/175 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/175' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)n1nc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C) `ZINC000538464030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000538464030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000538464030 none CC[C@H](C)n1nc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', '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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 5, 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] 0 hydrogens 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, 13, 5, 13, 13, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 5, 5, 5, 15, 15, 15, 15, 15, 13, 13, 13, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC000538464030 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030 Building ZINC000538464030 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000538464030 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 174) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC[C@H](C)n1nc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C) `ZINC000538464030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000538464030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000538464030 none CC[C@H](C)n1nc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', '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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 5, 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] 0 hydrogens 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, 11, 5, 11, 11, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 5, 5, 5, 13, 13, 13, 13, 13, 11, 11, 11, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 175) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC[C@H](C)n1nc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C) `ZINC000538464030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000538464030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000538464030 none CC[C@H](C)n1nc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', '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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 5, 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] 0 hydrogens 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, 13, 5, 13, 13, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 5, 5, 5, 15, 15, 15, 15, 15, 13, 13, 13, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC000538464030 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC000538464030 Building ZINC001359789777 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001359789777 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/176 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/176' -> `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(Sc2ccccc2)CCCC1) `ZINC001359789777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001359789777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001359789777 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(Sc2ccccc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 1, 1, 1, 1, 1, 1, 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] dock 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, 2, 2, 2, 18, 30, 46, 46, 46, 46, 46, 46, 30, 30, 30, 30, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 9, 9, 46, 46, 46, 46, 46, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/177 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/177' -> `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(Sc2ccccc2)CCCC1) `ZINC001359789777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001359789777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001359789777 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(Sc2ccccc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 1, 1, 1, 1, 1, 1, 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] dock 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: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 18, 30, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 9, 9, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001359789777 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777 Building ZINC001359789777 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001359789777 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 176) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(Sc2ccccc2)CCCC1) `ZINC001359789777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001359789777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001359789777 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(Sc2ccccc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 1, 1, 1, 1, 1, 1, 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] dock 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, 2, 2, 2, 18, 30, 46, 46, 46, 46, 46, 46, 30, 30, 30, 30, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 9, 9, 46, 46, 46, 46, 46, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 177) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(Sc2ccccc2)CCCC1) `ZINC001359789777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001359789777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001359789777 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(Sc2ccccc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 1, 1, 1, 1, 1, 1, 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] dock 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: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 18, 30, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 9, 9, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001359789777 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359789777 Building ZINC001359809868 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001359809868 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/178 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)c2ccccc2)cc1Br) `ZINC001359809868.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001359809868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001359809868 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 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, 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, 7, 7] 0 hydrogens 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, 36, 11, 36, 36, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 6, 12, 12, 6, 12, 12, 36, 36, 36, 50, 50, 50, 36, 36, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 36] 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]) total number of confs: 186 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/179 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/179' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)c2ccccc2)cc1Br) `ZINC001359809868.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001359809868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001359809868 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 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, 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, 7, 7] 0 hydrogens 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, 32, 12, 32, 32, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 6, 12, 12, 6, 12, 12, 32, 32, 32, 48, 48, 48, 32, 32, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 32] 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]) total number of confs: 177 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001359809868 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868 Building ZINC001359809868 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001359809868 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 178) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)c2ccccc2)cc1Br) `ZINC001359809868.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001359809868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001359809868 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 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, 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, 7, 7] 0 hydrogens 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, 36, 11, 36, 36, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 6, 12, 12, 6, 12, 12, 36, 36, 36, 50, 50, 50, 36, 36, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 36] 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]) total number of confs: 186 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 179) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)c2ccccc2)cc1Br) `ZINC001359809868.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001359809868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001359809868 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 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, 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, 7, 7] 0 hydrogens 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, 32, 12, 32, 32, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 6, 12, 12, 6, 12, 12, 32, 32, 32, 48, 48, 48, 32, 32, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 32] 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]) total number of confs: 177 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001359809868 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809868 Building ZINC001359809869 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001359809869 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/180 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)c2ccccc2)cc1Br) `ZINC001359809869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001359809869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001359809869 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 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, 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, 7, 7] 0 hydrogens 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, 33, 12, 33, 33, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 6, 12, 12, 6, 12, 12, 33, 33, 33, 49, 49, 49, 33, 33, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 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, 46, 47]) total number of confs: 180 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/181 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/181' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)c2ccccc2)cc1Br) `ZINC001359809869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001359809869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001359809869 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 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, 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, 7, 7] 0 hydrogens 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, 36, 11, 36, 36, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 12, 12, 6, 12, 12, 36, 36, 36, 49, 49, 49, 36, 36, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 36] 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]) total number of confs: 196 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001359809869 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869 Building ZINC001359809869 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001359809869 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 180) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)c2ccccc2)cc1Br) `ZINC001359809869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001359809869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001359809869 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 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, 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, 7, 7] 0 hydrogens 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, 33, 12, 33, 33, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 6, 12, 12, 6, 12, 12, 33, 33, 33, 49, 49, 49, 33, 33, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 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, 46, 47]) total number of confs: 180 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 181) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)c2ccccc2)cc1Br) `ZINC001359809869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001359809869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001359809869 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 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, 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, 7, 7] 0 hydrogens 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, 36, 11, 36, 36, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 12, 12, 6, 12, 12, 36, 36, 36, 49, 49, 49, 36, 36, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 36] 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]) total number of confs: 196 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001359809869 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359809869 Building ZINC001359817590 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001359817590 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/182 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1nccn1Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001359817590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001359817590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001359817590 none CC(C)c1nccn1Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 5, 5, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 49, 46, 46, 46, 46, 18, 5, 5, 2, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 49, 49, 49, 49, 49, 49, 49, 46, 46, 18, 18, 2, 5, 5, 2, 4, 4, 5] 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/183 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1nccn1Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001359817590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001359817590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001359817590 none CC(C)c1nccn1Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 5, 5, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 49, 47, 47, 47, 47, 19, 6, 6, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 6, 49, 49, 49, 49, 49, 49, 49, 47, 47, 19, 19, 3, 6, 6, 2, 4, 4, 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001359817590 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590 Building ZINC001359817590 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001359817590 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 182) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)c1nccn1Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001359817590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001359817590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001359817590 none CC(C)c1nccn1Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 5, 5, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 49, 46, 46, 46, 46, 18, 5, 5, 2, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 49, 49, 49, 49, 49, 49, 49, 46, 46, 18, 18, 2, 5, 5, 2, 4, 4, 5] 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 183) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)c1nccn1Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001359817590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001359817590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001359817590 none CC(C)c1nccn1Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 5, 5, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 49, 47, 47, 47, 47, 19, 6, 6, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 6, 49, 49, 49, 49, 49, 49, 49, 47, 47, 19, 19, 3, 6, 6, 2, 4, 4, 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001359817590 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359817590 Building ZINC001359847012 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001359847012 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/184 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001359847012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001359847012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001359847012 none CCN(CC)CCN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', '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.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 5, 12, 1, 1, 1, 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, 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] 0 hydrogens 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, 19, 5, 19, 22, 5, 2, 1, 2, 3, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 5, 5, 5, 5, 3, 3, 10, 10, 10, 1, 1, 1, 1] 50 rigid atoms, others: [49, 7, 50, 47, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 107 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/185 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/185' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001359847012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001359847012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001359847012 none CCN(CC)CCN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', '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.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 5, 12, 1, 1, 1, 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, 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] 0 hydrogens 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, 19, 6, 19, 25, 6, 3, 2, 3, 4, 9, 9, 9, 9, 9, 9, 9, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 25, 25, 25, 25, 25, 6, 6, 6, 6, 4, 4, 9, 9, 9, 1, 1, 1, 1] 50 rigid atoms, others: [49, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001359847012 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012 Building ZINC001359847012 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001359847012 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 184) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCN(CC)CCN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001359847012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001359847012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001359847012 none CCN(CC)CCN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', '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.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 5, 12, 1, 1, 1, 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, 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] 0 hydrogens 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, 19, 5, 19, 22, 5, 2, 1, 2, 3, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 5, 5, 5, 5, 3, 3, 10, 10, 10, 1, 1, 1, 1] 50 rigid atoms, others: [49, 7, 50, 47, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 107 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 185) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCN(CC)CCN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001359847012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001359847012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001359847012 none CCN(CC)CCN(Cc1ccc(Cl)c(Cl)c1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', '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.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 5, 12, 1, 1, 1, 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, 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] 0 hydrogens 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, 19, 6, 19, 25, 6, 3, 2, 3, 4, 9, 9, 9, 9, 9, 9, 9, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 25, 25, 25, 25, 25, 6, 6, 6, 6, 4, 4, 9, 9, 9, 1, 1, 1, 1] 50 rigid atoms, others: [49, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001359847012 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359847012 Building ZINC001359857318 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001359857318 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/186 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2c3ccccc3CC[C@H]2C(=O)Nc2ccccc2)cc1Cl) `ZINC001359857318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001359857318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001359857318 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2c3ccccc3CC[C@H]2C(=O)Nc2ccccc2)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.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.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, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 3, 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] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 28, 28, 17, 28, 28, 6, 6, 6, 15, 15, 15, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 17, 28, 28, 17, 28, 28, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/187 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2c3ccccc3CC[C@H]2C(=O)Nc2ccccc2)cc1Cl) `ZINC001359857318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001359857318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001359857318 none COc1ccc([C@]([O-])([SiH3])C(=O)N2c3ccccc3CC[C@H]2C(=O)Nc2ccccc2)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.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.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, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 3, 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] 0 hydrogens 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, 3, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 28, 28, 19, 28, 28, 4, 4, 4, 9, 9, 9, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 19, 28, 28, 19, 28, 28, 4] 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: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001359857318 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318 Building ZINC001359857318 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001359857318 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 186) grep: /scratch/xiaobo/182395/xbh-8058088.34/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@@]([O-])([SiH3])C(=O)N2c3ccccc3CC[C@H]2C(=O)Nc2ccccc2)cc1Cl) `ZINC001359857318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001359857318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001359857318 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2c3ccccc3CC[C@H]2C(=O)Nc2ccccc2)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.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.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, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 3, 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] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 28, 28, 17, 28, 28, 6, 6, 6, 15, 15, 15, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 17, 28, 28, 17, 28, 28, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 187) grep: /scratch/xiaobo/182395/xbh-8058088.34/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@]([O-])([SiH3])C(=O)N2c3ccccc3CC[C@H]2C(=O)Nc2ccccc2)cc1Cl) `ZINC001359857318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001359857318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001359857318 none COc1ccc([C@]([O-])([SiH3])C(=O)N2c3ccccc3CC[C@H]2C(=O)Nc2ccccc2)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.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.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, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 3, 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] 0 hydrogens 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, 3, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 28, 28, 19, 28, 28, 4, 4, 4, 9, 9, 9, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 19, 28, 28, 19, 28, 28, 4] 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: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001359857318 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857318 Building ZINC001359857319 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001359857319 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/188 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2c3ccccc3CC[C@@H]2C(=O)Nc2ccccc2)cc1Cl) `ZINC001359857319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001359857319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001359857319 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2c3ccccc3CC[C@@H]2C(=O)Nc2ccccc2)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.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.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, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 3, 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] 0 hydrogens 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, 2, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 26, 26, 26, 26, 26, 4, 4, 4, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 26, 26, 26, 26, 26, 4] 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/189 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/189' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2c3ccccc3CC[C@@H]2C(=O)Nc2ccccc2)cc1Cl) `ZINC001359857319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001359857319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001359857319 none COc1ccc([C@]([O-])([SiH3])C(=O)N2c3ccccc3CC[C@@H]2C(=O)Nc2ccccc2)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.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.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, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 3, 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] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 29, 29, 29, 29, 29, 6, 6, 6, 16, 16, 16, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 15, 29, 29, 29, 29, 29, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001359857319 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319 Building ZINC001359857319 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001359857319 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 188) grep: /scratch/xiaobo/182395/xbh-8058088.34/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@@]([O-])([SiH3])C(=O)N2c3ccccc3CC[C@@H]2C(=O)Nc2ccccc2)cc1Cl) `ZINC001359857319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001359857319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001359857319 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2c3ccccc3CC[C@@H]2C(=O)Nc2ccccc2)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.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.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, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 3, 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] 0 hydrogens 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, 2, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 26, 26, 26, 26, 26, 4, 4, 4, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 26, 26, 26, 26, 26, 4] 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 189) grep: /scratch/xiaobo/182395/xbh-8058088.34/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@]([O-])([SiH3])C(=O)N2c3ccccc3CC[C@@H]2C(=O)Nc2ccccc2)cc1Cl) `ZINC001359857319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001359857319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001359857319 none COc1ccc([C@]([O-])([SiH3])C(=O)N2c3ccccc3CC[C@@H]2C(=O)Nc2ccccc2)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.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.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, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 3, 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] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 29, 29, 29, 29, 29, 6, 6, 6, 16, 16, 16, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 15, 29, 29, 29, 29, 29, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001359857319 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359857319 Building ZINC001359942206 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001359942206 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/190 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/190' -> `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)(C)c1ccc(OCC(C)C)cc1) `ZINC001359942206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001359942206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001359942206 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)c1ccc(OCC(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.ar', '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', 'C.ar', 'C.ar', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 12, 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, 7, 7, 7, 7, 7, 7, 7] dock 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 13, 13, 6, 9, 37, 38, 50, 50, 13, 13, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 13, 13, 38, 38, 50, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 40, 41, 10, 12, 2, 14, 13, 11, 4, 15, 42] set([5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/191 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/191' -> `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)(C)c1ccc(OCC(C)C)cc1) `ZINC001359942206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001359942206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001359942206 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)c1ccc(OCC(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.ar', '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', 'C.ar', 'C.ar', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 12, 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, 7, 7, 7, 7, 7, 7, 7] dock 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 13, 13, 6, 9, 36, 38, 50, 50, 13, 13, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 13, 13, 38, 38, 50, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 40, 41, 10, 11, 12, 2, 14, 13, 4, 15, 42] set([5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001359942206 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206 Building ZINC001359942206 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001359942206 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 190) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)c1ccc(OCC(C)C)cc1) `ZINC001359942206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001359942206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001359942206 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)c1ccc(OCC(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.ar', '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', 'C.ar', 'C.ar', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 12, 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, 7, 7, 7, 7, 7, 7, 7] dock 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 13, 13, 6, 9, 37, 38, 50, 50, 13, 13, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 13, 13, 38, 38, 50, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 40, 41, 10, 12, 2, 14, 13, 11, 4, 15, 42] set([5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 191) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)c1ccc(OCC(C)C)cc1) `ZINC001359942206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001359942206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001359942206 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)c1ccc(OCC(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.ar', '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', 'C.ar', 'C.ar', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 12, 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, 7, 7, 7, 7, 7, 7, 7] dock 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 13, 13, 6, 9, 36, 38, 50, 50, 13, 13, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 13, 13, 38, 38, 50, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 40, 41, 10, 11, 12, 2, 14, 13, 4, 15, 42] set([5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001359942206 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001359942206 Building ZINC001360017835 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360017835 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/192 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)cc(N(CC(=O)Nc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC001360017835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360017835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001360017835 none Cc1cc(C)cc(N(CC(=O)Nc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 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, 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: [9, 9, 9, 9, 9, 9, 9, 5, 9, 14, 22, 22, 22, 28, 28, 22, 28, 28, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 22, 28, 28, 22, 28, 28, 6, 6, 6, 6, 6, 6, 6, 6, 6, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/193 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/193' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)cc(N(CC(=O)Nc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC001360017835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360017835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001360017835 none Cc1cc(C)cc(N(CC(=O)Nc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 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, 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: [10, 10, 9, 10, 10, 10, 9, 5, 9, 13, 21, 21, 21, 27, 27, 27, 27, 27, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 9, 10, 10, 10, 10, 13, 13, 21, 27, 27, 27, 27, 27, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360017835 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835 Building ZINC001360017835 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360017835 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 192) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(C)cc(N(CC(=O)Nc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC001360017835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360017835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001360017835 none Cc1cc(C)cc(N(CC(=O)Nc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 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, 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: [9, 9, 9, 9, 9, 9, 9, 5, 9, 14, 22, 22, 22, 28, 28, 22, 28, 28, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 22, 28, 28, 22, 28, 28, 6, 6, 6, 6, 6, 6, 6, 6, 6, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 193) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(C)cc(N(CC(=O)Nc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC001360017835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360017835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001360017835 none Cc1cc(C)cc(N(CC(=O)Nc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 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, 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: [10, 10, 9, 10, 10, 10, 9, 5, 9, 13, 21, 21, 21, 27, 27, 27, 27, 27, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 9, 10, 10, 10, 10, 13, 13, 21, 27, 27, 27, 27, 27, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360017835 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360017835 Building ZINC001360042608 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001360042608 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/194 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccc(C(C)(C)C)cc3)CC2)cc1Cl) `ZINC001360042608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360042608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360042608 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccc(C(C)(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.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 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, 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, 7] 0 hydrogens 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, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 15, 15, 15, 15, 28, 28, 28, 15, 15, 8, 8, 3, 3, 3, 6, 6, 6, 3, 3, 2, 8, 8, 8, 8, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 8, 8, 8, 8, 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/195 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/195' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccc(C(C)(C)C)cc3)CC2)cc1Cl) `ZINC001360042608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360042608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360042608 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccc(C(C)(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.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 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, 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, 7] 0 hydrogens 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, 3, 8, 8, 8, 8, 8, 15, 15, 15, 15, 27, 27, 27, 15, 15, 8, 8, 4, 4, 4, 7, 7, 7, 4, 4, 2, 8, 8, 8, 8, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 15, 15, 8, 8, 8, 8, 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/196 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/196' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccc(C(C)(C)C)cc3)CC2)cc1Cl) `ZINC001360042608.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001360042608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/2/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 62 natoms 61 natoms 60 natoms 59 names: ZINC001360042608 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccc(C(C)(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.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 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, 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, 7] 0 hydrogens 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, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 14, 14, 14, 14, 28, 28, 28, 14, 14, 8, 8, 3, 3, 3, 6, 6, 6, 3, 3, 2, 8, 8, 8, 8, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 8, 8, 8, 8, 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/197 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/197' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccc(C(C)(C)C)cc3)CC2)cc1Cl) `ZINC001360042608.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001360042608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/3/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 62 natoms 61 natoms 60 natoms 59 names: ZINC001360042608 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccc(C(C)(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.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 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, 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, 7] 0 hydrogens 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, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 14, 14, 14, 14, 27, 27, 27, 14, 14, 8, 8, 3, 3, 3, 6, 6, 6, 3, 3, 2, 8, 8, 8, 8, 14, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 14, 14, 8, 8, 8, 8, 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: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360042608 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 Building ZINC001360042608 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001360042608 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 194) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccc(C(C)(C)C)cc3)CC2)cc1Cl) `ZINC001360042608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360042608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360042608 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccc(C(C)(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.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 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, 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, 7] 0 hydrogens 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, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 15, 15, 15, 15, 28, 28, 28, 15, 15, 8, 8, 3, 3, 3, 6, 6, 6, 3, 3, 2, 8, 8, 8, 8, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 8, 8, 8, 8, 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 195) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccc(C(C)(C)C)cc3)CC2)cc1Cl) `ZINC001360042608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360042608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360042608 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccc(C(C)(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.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 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, 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, 7] 0 hydrogens 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, 3, 8, 8, 8, 8, 8, 15, 15, 15, 15, 27, 27, 27, 15, 15, 8, 8, 4, 4, 4, 7, 7, 7, 4, 4, 2, 8, 8, 8, 8, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 15, 15, 8, 8, 8, 8, 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 196) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/196: 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]2CC[N@](c3ccc(C(C)(C)C)cc3)CC2)cc1Cl) `ZINC001360042608.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001360042608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/2/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 62 natoms 61 natoms 60 natoms 59 names: ZINC001360042608 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccc(C(C)(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.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 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, 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, 7] 0 hydrogens 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, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 14, 14, 14, 14, 28, 28, 28, 14, 14, 8, 8, 3, 3, 3, 6, 6, 6, 3, 3, 2, 8, 8, 8, 8, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 8, 8, 8, 8, 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 197) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/197: 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]2CC[N@@](c3ccc(C(C)(C)C)cc3)CC2)cc1Cl) `ZINC001360042608.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001360042608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/3/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 62 natoms 61 natoms 60 natoms 59 names: ZINC001360042608 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccc(C(C)(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.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 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, 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, 7] 0 hydrogens 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, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 14, 14, 14, 14, 27, 27, 27, 14, 14, 8, 8, 3, 3, 3, 6, 6, 6, 3, 3, 2, 8, 8, 8, 8, 14, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 14, 14, 8, 8, 8, 8, 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: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360042608 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 Building ZINC001360042608 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001360042608 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 194) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccc(C(C)(C)C)cc3)CC2)cc1Cl) `ZINC001360042608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360042608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360042608 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccc(C(C)(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.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 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, 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, 7] 0 hydrogens 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, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 15, 15, 15, 15, 28, 28, 28, 15, 15, 8, 8, 3, 3, 3, 6, 6, 6, 3, 3, 2, 8, 8, 8, 8, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 8, 8, 8, 8, 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 195) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccc(C(C)(C)C)cc3)CC2)cc1Cl) `ZINC001360042608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360042608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360042608 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccc(C(C)(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.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 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, 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, 7] 0 hydrogens 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, 3, 8, 8, 8, 8, 8, 15, 15, 15, 15, 27, 27, 27, 15, 15, 8, 8, 4, 4, 4, 7, 7, 7, 4, 4, 2, 8, 8, 8, 8, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 15, 15, 8, 8, 8, 8, 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 196) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/196: 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]2CC[N@](c3ccc(C(C)(C)C)cc3)CC2)cc1Cl) `ZINC001360042608.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001360042608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/2/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 62 natoms 61 natoms 60 natoms 59 names: ZINC001360042608 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccc(C(C)(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.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 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, 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, 7] 0 hydrogens 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, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 14, 14, 14, 14, 28, 28, 28, 14, 14, 8, 8, 3, 3, 3, 6, 6, 6, 3, 3, 2, 8, 8, 8, 8, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 8, 8, 8, 8, 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 197) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/197: 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]2CC[N@@](c3ccc(C(C)(C)C)cc3)CC2)cc1Cl) `ZINC001360042608.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001360042608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/3/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 62 natoms 61 natoms 60 natoms 59 names: ZINC001360042608 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccc(C(C)(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.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 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, 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, 7] 0 hydrogens 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, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 14, 14, 14, 14, 27, 27, 27, 14, 14, 8, 8, 3, 3, 3, 6, 6, 6, 3, 3, 2, 8, 8, 8, 8, 14, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 14, 14, 8, 8, 8, 8, 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: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360042608 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 Building ZINC001360042608 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001360042608 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 194) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccc(C(C)(C)C)cc3)CC2)cc1Cl) `ZINC001360042608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360042608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360042608 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccc(C(C)(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.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 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, 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, 7] 0 hydrogens 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, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 15, 15, 15, 15, 28, 28, 28, 15, 15, 8, 8, 3, 3, 3, 6, 6, 6, 3, 3, 2, 8, 8, 8, 8, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 8, 8, 8, 8, 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 195) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccc(C(C)(C)C)cc3)CC2)cc1Cl) `ZINC001360042608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360042608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360042608 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccc(C(C)(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.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 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, 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, 7] 0 hydrogens 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, 3, 8, 8, 8, 8, 8, 15, 15, 15, 15, 27, 27, 27, 15, 15, 8, 8, 4, 4, 4, 7, 7, 7, 4, 4, 2, 8, 8, 8, 8, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 15, 15, 8, 8, 8, 8, 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 196) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/196: 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]2CC[N@](c3ccc(C(C)(C)C)cc3)CC2)cc1Cl) `ZINC001360042608.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001360042608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/2/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 62 natoms 61 natoms 60 natoms 59 names: ZINC001360042608 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccc(C(C)(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.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 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, 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, 7] 0 hydrogens 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, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 14, 14, 14, 14, 28, 28, 28, 14, 14, 8, 8, 3, 3, 3, 6, 6, 6, 3, 3, 2, 8, 8, 8, 8, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 8, 8, 8, 8, 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 197) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/197: 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]2CC[N@@](c3ccc(C(C)(C)C)cc3)CC2)cc1Cl) `ZINC001360042608.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001360042608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/3/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 62 natoms 61 natoms 60 natoms 59 names: ZINC001360042608 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccc(C(C)(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.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 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, 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, 7] 0 hydrogens 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, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 14, 14, 14, 14, 27, 27, 27, 14, 14, 8, 8, 3, 3, 3, 6, 6, 6, 3, 3, 2, 8, 8, 8, 8, 14, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 14, 14, 8, 8, 8, 8, 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: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360042608 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360042608 Building ZINC001360072427 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360072427 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/198 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1CS(=O)(=O)c1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001360072427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360072427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001360072427 none O=C(Nc1ccccc1CS(=O)(=O)c1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 3, 3, 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 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 15, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 15, 15, 15, 15, 15, 15, 37, 37, 37, 37, 37, 3, 1, 3] 44 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/199 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/199' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1CS(=O)(=O)c1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001360072427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360072427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001360072427 none O=C(Nc1ccccc1CS(=O)(=O)c1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 3, 3, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 14, 14, 14, 14, 14, 14, 14, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 6, 14, 14, 14, 14, 14, 14, 38, 38, 38, 38, 38, 4, 1, 4] 45 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360072427 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427 Building ZINC001360072427 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360072427 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 198) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1ccccc1CS(=O)(=O)c1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001360072427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360072427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001360072427 none O=C(Nc1ccccc1CS(=O)(=O)c1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 3, 3, 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 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 15, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 15, 15, 15, 15, 15, 15, 37, 37, 37, 37, 37, 3, 1, 3] 44 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 199) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1ccccc1CS(=O)(=O)c1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001360072427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360072427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001360072427 none O=C(Nc1ccccc1CS(=O)(=O)c1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 3, 3, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 14, 14, 14, 14, 14, 14, 14, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 6, 14, 14, 14, 14, 14, 14, 38, 38, 38, 38, 38, 4, 1, 4] 45 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360072427 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360072427 Building ZINC001360084535 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360084535 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/200 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCSC[C@@H]1c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360084535.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360084535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001360084535 none O=C(N1CCSC[C@@H]1c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [13, 2, 15, 19, 19, 19, 19, 19, 19, 19, 28, 28, 28, 28, 28, 28, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 19, 19, 19, 19, 28, 28, 28, 28, 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]) total number of confs: 64 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/201 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCSC[C@@H]1c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360084535.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360084535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001360084535 none O=C(N1CCSC[C@@H]1c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [13, 2, 16, 18, 18, 18, 18, 18, 18, 18, 24, 24, 18, 18, 24, 24, 1, 1, 1, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 24, 24, 24, 24, 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]) total number of confs: 74 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360084535 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535 Building ZINC001360084535 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360084535 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 200) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCSC[C@@H]1c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360084535.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360084535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001360084535 none O=C(N1CCSC[C@@H]1c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [13, 2, 15, 19, 19, 19, 19, 19, 19, 19, 28, 28, 28, 28, 28, 28, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 19, 19, 19, 19, 28, 28, 28, 28, 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]) total number of confs: 64 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 201) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCSC[C@@H]1c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360084535.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360084535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001360084535 none O=C(N1CCSC[C@@H]1c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [13, 2, 16, 18, 18, 18, 18, 18, 18, 18, 24, 24, 18, 18, 24, 24, 1, 1, 1, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 24, 24, 24, 24, 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]) total number of confs: 74 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360084535 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084535 Building ZINC001360084536 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360084536 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/202 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCSC[C@H]1c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360084536.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360084536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001360084536 none O=C(N1CCSC[C@H]1c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [11, 2, 14, 16, 16, 16, 16, 16, 16, 16, 24, 24, 16, 19, 24, 24, 1, 1, 1, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 16, 24, 24, 24, 24, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/203 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/203' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCSC[C@H]1c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360084536.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360084536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001360084536 none O=C(N1CCSC[C@H]1c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [12, 2, 14, 19, 19, 19, 19, 19, 19, 19, 27, 27, 19, 19, 27, 27, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 19, 19, 19, 19, 27, 27, 27, 27, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360084536 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536 Building ZINC001360084536 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360084536 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 202) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCSC[C@H]1c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360084536.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360084536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001360084536 none O=C(N1CCSC[C@H]1c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [11, 2, 14, 16, 16, 16, 16, 16, 16, 16, 24, 24, 16, 19, 24, 24, 1, 1, 1, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 16, 24, 24, 24, 24, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 203) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCSC[C@H]1c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360084536.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360084536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001360084536 none O=C(N1CCSC[C@H]1c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [12, 2, 14, 19, 19, 19, 19, 19, 19, 19, 27, 27, 19, 19, 27, 27, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 19, 19, 19, 19, 27, 27, 27, 27, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360084536 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360084536 Building ZINC001360099310 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360099310 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/204 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOc1ccc(OCc2ccccc2)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001360099310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360099310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001360099310 none CN(CCOc1ccc(OCc2ccccc2)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.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.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.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, 8, 5, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 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, 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] 0 hydrogens need 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, 5, 7, 16, 22, 22, 16, 16, 38, 38, 38, 38, 38, 38, 38, 22, 22, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 7, 7, 22, 22, 38, 38, 38, 38, 38, 38, 38, 22, 22, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 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: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/205 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOc1ccc(OCc2ccccc2)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001360099310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360099310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001360099310 none CN(CCOc1ccc(OCc2ccccc2)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.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.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.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, 8, 5, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 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, 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] 0 hydrogens need 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, 5, 7, 16, 22, 22, 16, 18, 38, 38, 38, 38, 38, 38, 38, 22, 22, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 7, 7, 22, 22, 38, 38, 38, 38, 38, 38, 38, 22, 22, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 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: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360099310 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310 Building ZINC001360099310 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360099310 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 204) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(CCOc1ccc(OCc2ccccc2)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001360099310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360099310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001360099310 none CN(CCOc1ccc(OCc2ccccc2)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.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.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.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, 8, 5, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 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, 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] 0 hydrogens need 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, 5, 7, 16, 22, 22, 16, 16, 38, 38, 38, 38, 38, 38, 38, 22, 22, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 7, 7, 22, 22, 38, 38, 38, 38, 38, 38, 38, 22, 22, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 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: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 205) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(CCOc1ccc(OCc2ccccc2)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001360099310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360099310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001360099310 none CN(CCOc1ccc(OCc2ccccc2)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.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.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.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, 8, 5, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 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, 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] 0 hydrogens need 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, 5, 7, 16, 22, 22, 16, 18, 38, 38, 38, 38, 38, 38, 38, 22, 22, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 7, 7, 22, 22, 38, 38, 38, 38, 38, 38, 38, 22, 22, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 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: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360099310 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360099310 Building ZINC001360106284 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360106284 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/206 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(O[C@@H]2CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1) `ZINC001360106284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360106284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360106284 none CCCOc1ccc(O[C@@H]2CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 5, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 7, 7, 7, 7, 5, 4, 4, 4, 4, 4, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 10, 4, 4, 4, 7, 7, 27, 27, 27, 27, 27, 16, 16, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 10, 10, 10, 4, 7, 7] 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/207 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/207' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(O[C@@H]2CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1) `ZINC001360106284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360106284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360106284 none CCCOc1ccc(O[C@@H]2CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 5, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 8, 8, 9, 9, 6, 5, 5, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 11, 4, 4, 4, 9, 9, 33, 33, 33, 33, 33, 18, 18, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 11, 11, 11, 4, 9, 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, 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/182395/xbh-8058088.34/working/building/ZINC001360106284 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360106284 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284 Building ZINC001360106284 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360106284 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 206) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCOc1ccc(O[C@@H]2CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1) `ZINC001360106284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360106284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360106284 none CCCOc1ccc(O[C@@H]2CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 5, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 7, 7, 7, 7, 5, 4, 4, 4, 4, 4, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 10, 4, 4, 4, 7, 7, 27, 27, 27, 27, 27, 16, 16, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 10, 10, 10, 4, 7, 7] 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 207) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCOc1ccc(O[C@@H]2CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1) `ZINC001360106284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360106284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360106284 none CCCOc1ccc(O[C@@H]2CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 5, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 8, 8, 9, 9, 6, 5, 5, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 11, 4, 4, 4, 9, 9, 33, 33, 33, 33, 33, 18, 18, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 11, 11, 11, 4, 9, 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, 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/182395/xbh-8058088.34/working/building/ZINC001360106284 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360106284 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106284 Building ZINC001360106285 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360106285 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/208 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(O[C@H]2CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1) `ZINC001360106285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360106285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360106285 none CCCOc1ccc(O[C@H]2CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 5, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 7, 7, 9, 9, 7, 4, 4, 4, 4, 4, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 9, 9, 27, 27, 27, 27, 27, 16, 16, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 9, 9, 9, 4, 9, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/209 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(O[C@H]2CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1) `ZINC001360106285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360106285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360106285 none CCCOc1ccc(O[C@H]2CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 5, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 8, 8, 10, 10, 6, 4, 4, 4, 4, 4, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 2, 6, 14, 6, 6, 6, 10, 10, 35, 35, 35, 35, 35, 23, 23, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 2, 6, 6, 14, 14, 14, 6, 10, 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, 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/182395/xbh-8058088.34/working/building/ZINC001360106285 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360106285 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285 Building ZINC001360106285 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360106285 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 208) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/208: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(O[C@H]2CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1) `ZINC001360106285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360106285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360106285 none CCCOc1ccc(O[C@H]2CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 5, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 7, 7, 9, 9, 7, 4, 4, 4, 4, 4, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 9, 9, 27, 27, 27, 27, 27, 16, 16, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 9, 9, 9, 4, 9, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 209) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/209: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(O[C@H]2CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1) `ZINC001360106285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360106285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360106285 none CCCOc1ccc(O[C@H]2CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 5, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 8, 8, 10, 10, 6, 4, 4, 4, 4, 4, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 2, 6, 14, 6, 6, 6, 10, 10, 35, 35, 35, 35, 35, 23, 23, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 2, 6, 6, 14, 14, 14, 6, 10, 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, 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/182395/xbh-8058088.34/working/building/ZINC001360106285 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360106285 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106285 Building ZINC001360106286 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360106286 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/210 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(O[C@@H]2CCCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1) `ZINC001360106286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360106286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360106286 none CCCOc1ccc(O[C@@H]2CCCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 5, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 6, 6, 10, 10, 6, 4, 4, 4, 4, 4, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 3, 6, 14, 6, 6, 6, 10, 10, 33, 33, 33, 33, 33, 23, 23, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 2, 6, 6, 14, 14, 14, 6, 10, 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, 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/182395/xbh-8058088.34/working/building/ZINC001360106286 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/211 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(O[C@@H]2CCCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1) `ZINC001360106286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360106286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360106286 none CCCOc1ccc(O[C@@H]2CCCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 5, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 7, 7, 9, 9, 7, 4, 4, 4, 4, 4, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 9, 9, 27, 27, 27, 27, 27, 16, 16, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 9, 9, 9, 4, 9, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360106286 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286 Building ZINC001360106286 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360106286 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 210) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCOc1ccc(O[C@@H]2CCCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1) `ZINC001360106286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360106286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360106286 none CCCOc1ccc(O[C@@H]2CCCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 5, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 6, 6, 10, 10, 6, 4, 4, 4, 4, 4, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 3, 6, 14, 6, 6, 6, 10, 10, 33, 33, 33, 33, 33, 23, 23, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 2, 6, 6, 14, 14, 14, 6, 10, 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, 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/182395/xbh-8058088.34/working/building/ZINC001360106286 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 211) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCOc1ccc(O[C@@H]2CCCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1) `ZINC001360106286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360106286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360106286 none CCCOc1ccc(O[C@@H]2CCCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 5, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 7, 7, 9, 9, 7, 4, 4, 4, 4, 4, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 9, 9, 27, 27, 27, 27, 27, 16, 16, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 9, 9, 9, 4, 9, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360106286 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106286 Building ZINC001360106287 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360106287 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/212 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(O[C@H]2CCCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1) `ZINC001360106287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360106287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360106287 none CCCOc1ccc(O[C@H]2CCCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 5, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 6, 11, 11, 6, 5, 5, 5, 5, 5, 5, 5, 3, 5, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 11, 4, 4, 4, 11, 11, 35, 35, 35, 35, 35, 18, 18, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 11, 11, 11, 4, 11, 11] 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/213 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/213' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(O[C@H]2CCCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1) `ZINC001360106287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360106287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360106287 none CCCOc1ccc(O[C@H]2CCCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 5, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 6, 5, 8, 8, 5, 4, 4, 4, 4, 4, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 10, 4, 4, 4, 8, 8, 29, 29, 29, 29, 29, 17, 17, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 10, 10, 10, 4, 8, 8] 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360106287 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287 Building ZINC001360106287 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360106287 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 212) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/212: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(O[C@H]2CCCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1) `ZINC001360106287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360106287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360106287 none CCCOc1ccc(O[C@H]2CCCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 5, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 6, 11, 11, 6, 5, 5, 5, 5, 5, 5, 5, 3, 5, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 11, 4, 4, 4, 11, 11, 35, 35, 35, 35, 35, 18, 18, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 11, 11, 11, 4, 11, 11] 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 213) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/213: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(O[C@H]2CCCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1) `ZINC001360106287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360106287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360106287 none CCCOc1ccc(O[C@H]2CCCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 5, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 6, 5, 8, 8, 5, 4, 4, 4, 4, 4, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 10, 4, 4, 4, 8, 8, 29, 29, 29, 29, 29, 17, 17, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 10, 10, 10, 4, 8, 8] 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360106287 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360106287 Building ZINC001360134484 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360134484 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/214 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@@H]1C=CCC1)Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360134484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360134484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360134484 none O=C(C[C@@H]1C=CCC1)Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', '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', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 9, 41, 43, 43, 43, 43, 43, 7, 7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 38, 38, 43, 43, 43, 43, 43, 43, 9, 7, 7, 7, 7, 3, 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/215 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@@H]1C=CCC1)Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360134484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360134484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360134484 none O=C(C[C@@H]1C=CCC1)Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', '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', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 43, 45, 45, 45, 45, 45, 8, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 43, 43, 45, 45, 45, 45, 45, 45, 10, 8, 8, 8, 8, 3, 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360134484 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484 Building ZINC001360134484 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360134484 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 214) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(C[C@@H]1C=CCC1)Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360134484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360134484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360134484 none O=C(C[C@@H]1C=CCC1)Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', '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', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 9, 41, 43, 43, 43, 43, 43, 7, 7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 38, 38, 43, 43, 43, 43, 43, 43, 9, 7, 7, 7, 7, 3, 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 215) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(C[C@@H]1C=CCC1)Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360134484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360134484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360134484 none O=C(C[C@@H]1C=CCC1)Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', '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', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 43, 45, 45, 45, 45, 45, 8, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 43, 43, 45, 45, 45, 45, 45, 45, 10, 8, 8, 8, 8, 3, 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360134484 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134484 Building ZINC001360134487 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360134487 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/216 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@H]1C=CCC1)Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360134487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360134487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360134487 none O=C(C[C@H]1C=CCC1)Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', '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', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 42, 45, 45, 45, 45, 45, 8, 8, 8, 5, 8, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 42, 42, 45, 45, 45, 45, 45, 45, 10, 8, 8, 8, 8, 3, 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/217 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@H]1C=CCC1)Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360134487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360134487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360134487 none O=C(C[C@H]1C=CCC1)Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', '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', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 9, 43, 45, 45, 45, 45, 45, 7, 7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 40, 40, 45, 45, 45, 45, 45, 45, 9, 7, 7, 7, 7, 3, 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360134487 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487 Building ZINC001360134487 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360134487 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 216) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(C[C@H]1C=CCC1)Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360134487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360134487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360134487 none O=C(C[C@H]1C=CCC1)Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', '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', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 42, 45, 45, 45, 45, 45, 8, 8, 8, 5, 8, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 42, 42, 45, 45, 45, 45, 45, 45, 10, 8, 8, 8, 8, 3, 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 217) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(C[C@H]1C=CCC1)Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360134487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360134487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360134487 none O=C(C[C@H]1C=CCC1)Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', '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', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 9, 43, 45, 45, 45, 45, 45, 7, 7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 40, 40, 45, 45, 45, 45, 45, 45, 9, 7, 7, 7, 7, 3, 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360134487 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360134487 Building ZINC001360141693 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360141693 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/218 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@H]2CCc3ccccc3N2C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cc1) `ZINC001360141693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360141693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360141693 none Cc1ccc(NC(=O)[C@H]2CCc3ccccc3N2C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)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', 'H', 'C.3', 'C.3', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 31, 31, 27, 27, 12, 27, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 2, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 27, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 31, 31] 32 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]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/219 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/219' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@H]2CCc3ccccc3N2C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cc1) `ZINC001360141693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360141693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360141693 none Cc1ccc(NC(=O)[C@H]2CCc3ccccc3N2C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)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', 'H', 'C.3', 'C.3', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 39, 39, 31, 31, 13, 31, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 2, 12, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 31, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5, 5, 5, 5, 39, 39] 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]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360141693 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693 Building ZINC001360141693 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360141693 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 218) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(NC(=O)[C@H]2CCc3ccccc3N2C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cc1) `ZINC001360141693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360141693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360141693 none Cc1ccc(NC(=O)[C@H]2CCc3ccccc3N2C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)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', 'H', 'C.3', 'C.3', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 31, 31, 27, 27, 12, 27, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 2, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 27, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 31, 31] 32 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]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 219) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(NC(=O)[C@H]2CCc3ccccc3N2C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cc1) `ZINC001360141693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360141693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360141693 none Cc1ccc(NC(=O)[C@H]2CCc3ccccc3N2C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)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', 'H', 'C.3', 'C.3', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 39, 39, 31, 31, 13, 31, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 2, 12, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 31, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5, 5, 5, 5, 39, 39] 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]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360141693 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141693 Building ZINC001360141698 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360141698 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/220 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@H]2CCc3ccccc3N2C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cc1) `ZINC001360141698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360141698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360141698 none Cc1ccc(NC(=O)[C@@H]2CCc3ccccc3N2C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)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', 'H', 'C.3', 'C.3', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 41, 41, 37, 37, 12, 37, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 10, 3, 10, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 41, 41, 41, 41, 41, 41, 41, 37, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 5, 41, 41] 47 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]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/221 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/221' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@H]2CCc3ccccc3N2C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cc1) `ZINC001360141698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360141698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360141698 none Cc1ccc(NC(=O)[C@@H]2CCc3ccccc3N2C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)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', 'H', 'C.3', 'C.3', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 32, 32, 14, 32, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 3, 12, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 40, 40, 40, 40, 40, 40, 40, 32, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 5, 40, 40] 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]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360141698 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698 Building ZINC001360141698 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360141698 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 220) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/220: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H]2CCc3ccccc3N2C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cc1) `ZINC001360141698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360141698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360141698 none Cc1ccc(NC(=O)[C@@H]2CCc3ccccc3N2C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)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', 'H', 'C.3', 'C.3', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 41, 41, 37, 37, 12, 37, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 10, 3, 10, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 41, 41, 41, 41, 41, 41, 41, 37, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 5, 41, 41] 47 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]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 221) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/221: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H]2CCc3ccccc3N2C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cc1) `ZINC001360141698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360141698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360141698 none Cc1ccc(NC(=O)[C@@H]2CCc3ccccc3N2C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)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', 'H', 'C.3', 'C.3', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 32, 32, 14, 32, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 3, 12, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 40, 40, 40, 40, 40, 40, 40, 32, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 5, 40, 40] 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]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360141698 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360141698 Building ZINC001360206355 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360206355 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/222 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)cc(N(CC(=O)Nc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c1) `ZINC001360206355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360206355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001360206355 none Cc1cc(C)cc(N(CC(=O)Nc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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.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'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 12, 13, 13, 13, 12, 6, 12, 19, 28, 28, 28, 32, 32, 28, 32, 32, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 13, 13, 13, 13, 12, 13, 13, 13, 13, 19, 19, 28, 32, 32, 28, 32, 32, 9, 9, 13] 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]) total number of confs: 125 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/223 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)cc(N(CC(=O)Nc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c1) `ZINC001360206355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360206355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001360206355 none Cc1cc(C)cc(N(CC(=O)Nc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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.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'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 10, 5, 10, 17, 26, 26, 26, 31, 31, 31, 31, 31, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 26, 31, 31, 31, 31, 31, 9, 9, 11] 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]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360206355 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355 Building ZINC001360206355 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360206355 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 222) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(C)cc(N(CC(=O)Nc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c1) `ZINC001360206355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360206355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001360206355 none Cc1cc(C)cc(N(CC(=O)Nc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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.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'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 12, 13, 13, 13, 12, 6, 12, 19, 28, 28, 28, 32, 32, 28, 32, 32, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 13, 13, 13, 13, 12, 13, 13, 13, 13, 19, 19, 28, 32, 32, 28, 32, 32, 9, 9, 13] 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]) total number of confs: 125 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 223) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(C)cc(N(CC(=O)Nc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c1) `ZINC001360206355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360206355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001360206355 none Cc1cc(C)cc(N(CC(=O)Nc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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.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'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 10, 5, 10, 17, 26, 26, 26, 31, 31, 31, 31, 31, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 26, 31, 31, 31, 31, 31, 9, 9, 11] 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]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360206355 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360206355 Building ZINC001360209050 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360209050 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/224 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Oc2ccccc2C(F)(F)F)nc1) `ZINC001360209050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360209050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360209050 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Oc2ccccc2C(F)(F)F)nc1 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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.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, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 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, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in 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, 13, 29, 29, 29, 29, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 2, 2, 2, 2, 2, 2, 3, 13, 13, 29, 29, 50, 50, 50, 50, 29] 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: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/225 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1ccc(Oc2ccccc2C(F)(F)F)nc1) `ZINC001360209050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360209050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360209050 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1ccc(Oc2ccccc2C(F)(F)F)nc1 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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.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, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 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, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in 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, 13, 29, 29, 29, 29, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 2, 2, 2, 2, 2, 2, 3, 13, 13, 29, 29, 50, 50, 50, 50, 29] 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: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360209050 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050 Building ZINC001360209050 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360209050 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 224) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/224: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Oc2ccccc2C(F)(F)F)nc1) `ZINC001360209050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360209050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360209050 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Oc2ccccc2C(F)(F)F)nc1 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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.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, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 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, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in 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, 13, 29, 29, 29, 29, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 2, 2, 2, 2, 2, 2, 3, 13, 13, 29, 29, 50, 50, 50, 50, 29] 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: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 225) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/225: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Oc2ccccc2C(F)(F)F)nc1) `ZINC001360209050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360209050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360209050 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1ccc(Oc2ccccc2C(F)(F)F)nc1 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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.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, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 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, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in 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, 13, 29, 29, 29, 29, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 2, 2, 2, 2, 2, 2, 3, 13, 13, 29, 29, 50, 50, 50, 50, 29] 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: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360209050 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360209050 Building ZINC001360216554 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360216554 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/226 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cc3ccccc3o2)c1) `ZINC001360216554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360216554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360216554 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cc3ccccc3o2)c1 NO_LONG_NAME dock atom types: ['C.3', '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', '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.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, 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, 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, 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] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 15, 21, 21, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 2, 4, 4, 2, 6, 6, 6, 6, 15, 15, 21, 21, 21, 27, 27, 27, 27, 27, 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]) total number of confs: 105 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/227 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/227' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cc3ccccc3o2)c1) `ZINC001360216554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360216554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360216554 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cc3ccccc3o2)c1 NO_LONG_NAME dock atom types: ['C.3', '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', '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.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, 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, 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, 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] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 6, 6, 6, 14, 20, 20, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 4, 2, 4, 4, 2, 6, 6, 2, 6, 14, 14, 20, 20, 20, 26, 26, 26, 26, 26, 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]) total number of confs: 105 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360216554 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554 Building ZINC001360216554 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360216554 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 226) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cc3ccccc3o2)c1) `ZINC001360216554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360216554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360216554 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cc3ccccc3o2)c1 NO_LONG_NAME dock atom types: ['C.3', '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', '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.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, 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, 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, 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] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 15, 21, 21, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 2, 4, 4, 2, 6, 6, 6, 6, 15, 15, 21, 21, 21, 27, 27, 27, 27, 27, 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]) total number of confs: 105 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 227) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cc3ccccc3o2)c1) `ZINC001360216554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360216554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360216554 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cc3ccccc3o2)c1 NO_LONG_NAME dock atom types: ['C.3', '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', '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.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, 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, 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, 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] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 6, 6, 6, 14, 20, 20, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 4, 2, 4, 4, 2, 6, 6, 2, 6, 14, 14, 20, 20, 20, 26, 26, 26, 26, 26, 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]) total number of confs: 105 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360216554 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360216554 Building ZINC001360220776 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360220776 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/228 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1cc(C)c(OCc2ccc(C)cc2)c(C)c1)C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC001360220776.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360220776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001360220776 none CCN(Cc1cc(C)c(OCc2ccc(C)cc2)c(C)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.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 5, 1, 12, 5, 1, 1, 1, 1, 5, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 8, 24, 38, 38, 25, 29, 38, 38, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 24, 24, 38, 38, 38, 38, 38, 38, 38, 4, 4, 4, 4, 2, 5, 5, 5, 5, 5, 2] 50 rigid atoms, others: [0, 1, 34, 35, 32, 37, 38, 33, 2, 3, 25, 21, 22, 23, 24, 36, 4] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 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: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/229 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/229' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1cc(C)c(OCc2ccc(C)cc2)c(C)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC001360220776.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360220776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001360220776 none CCN(Cc1cc(C)c(OCc2ccc(C)cc2)c(C)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.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 5, 1, 12, 5, 1, 1, 1, 1, 5, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 2, 8, 25, 40, 40, 29, 40, 40, 40, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 25, 25, 40, 40, 40, 40, 40, 40, 40, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 2] 50 rigid atoms, others: [0, 1, 34, 35, 32, 37, 38, 33, 2, 3, 25, 21, 22, 23, 24, 36, 4] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 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: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360220776 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776 Building ZINC001360220776 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360220776 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 228) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCN(Cc1cc(C)c(OCc2ccc(C)cc2)c(C)c1)C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC001360220776.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360220776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001360220776 none CCN(Cc1cc(C)c(OCc2ccc(C)cc2)c(C)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.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 5, 1, 12, 5, 1, 1, 1, 1, 5, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 8, 24, 38, 38, 25, 29, 38, 38, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 24, 24, 38, 38, 38, 38, 38, 38, 38, 4, 4, 4, 4, 2, 5, 5, 5, 5, 5, 2] 50 rigid atoms, others: [0, 1, 34, 35, 32, 37, 38, 33, 2, 3, 25, 21, 22, 23, 24, 36, 4] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 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: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 229) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCN(Cc1cc(C)c(OCc2ccc(C)cc2)c(C)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC001360220776.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360220776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001360220776 none CCN(Cc1cc(C)c(OCc2ccc(C)cc2)c(C)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.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 5, 1, 12, 5, 1, 1, 1, 1, 5, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 2, 8, 25, 40, 40, 29, 40, 40, 40, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 25, 25, 40, 40, 40, 40, 40, 40, 40, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 2] 50 rigid atoms, others: [0, 1, 34, 35, 32, 37, 38, 33, 2, 3, 25, 21, 22, 23, 24, 36, 4] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 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: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360220776 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360220776 Building ZINC001360239961 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360239961 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/230 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Br)ccc1n1cccn1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001360239961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360239961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001360239961 none O=C(Nc1cc(Br)ccc1n1cccn1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 17, 1, 1, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 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: [6, 1, 6, 6, 21, 21, 21, 6, 21, 21, 21, 40, 40, 40, 40, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 6, 21, 21, 21, 40, 40, 40, 4, 1, 4] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/231 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/231' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Br)ccc1n1cccn1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001360239961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360239961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001360239961 none O=C(Nc1cc(Br)ccc1n1cccn1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 17, 1, 1, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 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: [6, 1, 6, 6, 20, 20, 20, 6, 20, 20, 20, 40, 40, 40, 40, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 6, 20, 20, 20, 40, 40, 40, 4, 1, 4] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360239961 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961 Building ZINC001360239961 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360239961 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 230) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cc(Br)ccc1n1cccn1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001360239961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360239961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001360239961 none O=C(Nc1cc(Br)ccc1n1cccn1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 17, 1, 1, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 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: [6, 1, 6, 6, 21, 21, 21, 6, 21, 21, 21, 40, 40, 40, 40, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 6, 21, 21, 21, 40, 40, 40, 4, 1, 4] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 231) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cc(Br)ccc1n1cccn1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001360239961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360239961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001360239961 none O=C(Nc1cc(Br)ccc1n1cccn1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 17, 1, 1, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 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: [6, 1, 6, 6, 20, 20, 20, 6, 20, 20, 20, 40, 40, 40, 40, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 6, 20, 20, 20, 40, 40, 40, 4, 1, 4] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360239961 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360239961 Building ZINC001360256322 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360256322 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/232 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/232' -> `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)NCC(C)(C)c1ccc(F)cc1Cl) `ZINC001360256322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360256322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001360256322 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 16, 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] 0 hydrogens need rotated 50 conformations in 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, 2, 12, 40, 41, 41, 42, 42, 41, 42, 42, 42, 42, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 12, 12, 41, 41, 41, 41, 41, 41, 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, 52]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/233 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/233' -> `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)NCC(C)(C)c1ccc(F)cc1Cl) `ZINC001360256322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360256322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001360256322 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 16, 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] 0 hydrogens need rotated 50 conformations in 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, 12, 42, 41, 42, 43, 43, 42, 43, 43, 43, 43, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 12, 12, 42, 42, 42, 42, 42, 42, 43, 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, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360256322 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322 Building ZINC001360256322 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360256322 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 232) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(F)cc1Cl) `ZINC001360256322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360256322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001360256322 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 16, 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] 0 hydrogens need rotated 50 conformations in 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, 2, 12, 40, 41, 41, 42, 42, 41, 42, 42, 42, 42, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 12, 12, 41, 41, 41, 41, 41, 41, 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, 52]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 233) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(F)cc1Cl) `ZINC001360256322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360256322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001360256322 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 16, 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] 0 hydrogens need rotated 50 conformations in 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, 12, 42, 41, 42, 43, 43, 42, 43, 43, 43, 43, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 12, 12, 42, 42, 42, 42, 42, 42, 43, 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, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360256322 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360256322 Building ZINC001360278772 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360278772 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/234 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCCc3c(NC(=O)Nc4ccccc4F)cccc32)c1) `ZINC001360278772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360278772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360278772 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCCc3c(NC(=O)Nc4ccccc4F)cccc32)c1 NO_LONG_NAME dock atom types: ['C.3', '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.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.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, 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, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 11, 12, 12, 13, 28, 28, 28, 28, 28, 28, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 11, 13, 28, 28, 28, 28, 3, 3, 3, 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, 53]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/235 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/235' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCCc3c(NC(=O)Nc4ccccc4F)cccc32)c1) `ZINC001360278772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360278772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360278772 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCCc3c(NC(=O)Nc4ccccc4F)cccc32)c1 NO_LONG_NAME dock atom types: ['C.3', '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.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.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, 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, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 10, 11, 11, 12, 27, 27, 18, 27, 27, 27, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 10, 12, 27, 27, 27, 27, 3, 3, 3, 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, 53]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360278772 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772 Building ZINC001360278772 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360278772 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 234) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCCc3c(NC(=O)Nc4ccccc4F)cccc32)c1) `ZINC001360278772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360278772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360278772 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCCc3c(NC(=O)Nc4ccccc4F)cccc32)c1 NO_LONG_NAME dock atom types: ['C.3', '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.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.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, 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, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 11, 12, 12, 13, 28, 28, 28, 28, 28, 28, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 11, 13, 28, 28, 28, 28, 3, 3, 3, 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, 53]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 235) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCCc3c(NC(=O)Nc4ccccc4F)cccc32)c1) `ZINC001360278772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360278772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360278772 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCCc3c(NC(=O)Nc4ccccc4F)cccc32)c1 NO_LONG_NAME dock atom types: ['C.3', '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.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.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, 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, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 10, 11, 11, 12, 27, 27, 18, 27, 27, 27, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 10, 12, 27, 27, 27, 27, 3, 3, 3, 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, 53]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360278772 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360278772 Building ZINC001360327390 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360327390 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/236 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/236' -> `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)N1CCCc2c(C)cccc21) `ZINC001360327390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360327390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001360327390 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2c(C)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', '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'] dock atom type 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, 1, 1, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 28, 28, 4, 28, 28, 28, 28, 28, 28, 3, 3, 1, 1, 1, 3, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 28, 28, 7, 28, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 94 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/237 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/237' -> `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)N1CCCc2c(C)cccc21) `ZINC001360327390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360327390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001360327390 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(C)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', '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'] dock atom type 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, 1, 1, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 29, 29, 4, 29, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 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, 52, 53]) total number of confs: 90 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360327390 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390 Building ZINC001360327390 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360327390 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 236) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCCc2c(C)cccc21) `ZINC001360327390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360327390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001360327390 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2c(C)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', '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'] dock atom type 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, 1, 1, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 28, 28, 4, 28, 28, 28, 28, 28, 28, 3, 3, 1, 1, 1, 3, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 28, 28, 7, 28, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 94 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 237) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCCc2c(C)cccc21) `ZINC001360327390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360327390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001360327390 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(C)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', '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'] dock atom type 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, 1, 1, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 29, 29, 4, 29, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 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, 52, 53]) total number of confs: 90 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360327390 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360327390 Building ZINC001360365055 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360365055 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/238 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1)c1ccc(C(F)(F)F)cc1) `ZINC001360365055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360365055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001360365055 none O=C(NCc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 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: [29, 29, 23, 8, 4, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 23, 23, 9, 9, 2, 2, 2, 2, 2, 9, 9, 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/239 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/239' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1)c1ccc(C(F)(F)F)cc1) `ZINC001360365055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360365055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001360365055 none O=C(NCc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 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: [29, 29, 23, 8, 4, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 29, 50, 50, 30, 44, 50, 50, 50, 50, 50, 29, 23, 23, 9, 9, 2, 2, 2, 2, 2, 9, 9, 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]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360365055 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055 Building ZINC001360365055 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360365055 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 238) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1)c1ccc(C(F)(F)F)cc1) `ZINC001360365055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360365055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001360365055 none O=C(NCc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 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: [29, 29, 23, 8, 4, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 23, 23, 9, 9, 2, 2, 2, 2, 2, 9, 9, 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 239) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1)c1ccc(C(F)(F)F)cc1) `ZINC001360365055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360365055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001360365055 none O=C(NCc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 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: [29, 29, 23, 8, 4, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 29, 50, 50, 30, 44, 50, 50, 50, 50, 50, 29, 23, 23, 9, 9, 2, 2, 2, 2, 2, 9, 9, 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]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360365055 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360365055 Building ZINC001360430150 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360430150 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/240 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cccc(Br)c2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001360430150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360430150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001360430150 none O=C(NCC1(c2cccc(Br)c2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 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] 0 hydrogens need 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, 14, 30, 50, 50, 50, 50, 50, 50, 30, 30, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 14, 14, 50, 50, 50, 50, 30, 30, 30, 30, 2, 1, 2] 50 rigid atoms, others: [1, 14, 15, 16] 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/241 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/241' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cccc(Br)c2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001360430150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360430150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001360430150 none O=C(NCC1(c2cccc(Br)c2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 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] 0 hydrogens need 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, 14, 31, 50, 50, 50, 50, 50, 50, 31, 31, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 14, 14, 50, 50, 50, 50, 31, 31, 31, 31, 3, 1, 3] 50 rigid atoms, others: [1, 14, 15, 16] 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360430150 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150 Building ZINC001360430150 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360430150 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 240) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NCC1(c2cccc(Br)c2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001360430150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360430150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001360430150 none O=C(NCC1(c2cccc(Br)c2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 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] 0 hydrogens need 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, 14, 30, 50, 50, 50, 50, 50, 50, 30, 30, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 14, 14, 50, 50, 50, 50, 30, 30, 30, 30, 2, 1, 2] 50 rigid atoms, others: [1, 14, 15, 16] 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 241) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NCC1(c2cccc(Br)c2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001360430150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360430150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001360430150 none O=C(NCC1(c2cccc(Br)c2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 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] 0 hydrogens need 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, 14, 31, 50, 50, 50, 50, 50, 50, 31, 31, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 14, 14, 50, 50, 50, 50, 31, 31, 31, 31, 3, 1, 3] 50 rigid atoms, others: [1, 14, 15, 16] 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360430150 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360430150 Building ZINC001360441551 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360441551 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/242 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCN(CC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001360441551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360441551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001360441551 none COc1ccc(CCN(CC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 12, 1, 1, 1, 1, 5, 5, 8, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 3, 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] 0 hydrogens 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, 17, 27, 27, 17, 14, 8, 5, 8, 9, 15, 15, 15, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 17, 17, 14, 14, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 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, 49]) total number of confs: 177 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/243 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/243' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCN(CC(C)(C)C)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001360441551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360441551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001360441551 none COc1ccc(CCN(CC(C)(C)C)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 12, 1, 1, 1, 1, 5, 5, 8, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 3, 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] 0 hydrogens 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, 23, 29, 29, 16, 13, 7, 4, 7, 8, 14, 14, 14, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 16, 16, 13, 13, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 9, 9, 29, 29] 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]) total number of confs: 152 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360441551 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551 Building ZINC001360441551 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360441551 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 242) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc(CCN(CC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001360441551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360441551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001360441551 none COc1ccc(CCN(CC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 12, 1, 1, 1, 1, 5, 5, 8, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 3, 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] 0 hydrogens 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, 17, 27, 27, 17, 14, 8, 5, 8, 9, 15, 15, 15, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 17, 17, 14, 14, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 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, 49]) total number of confs: 177 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 243) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc(CCN(CC(C)(C)C)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001360441551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360441551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001360441551 none COc1ccc(CCN(CC(C)(C)C)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 12, 1, 1, 1, 1, 5, 5, 8, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 3, 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] 0 hydrogens 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, 23, 29, 29, 16, 13, 7, 4, 7, 8, 14, 14, 14, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 16, 16, 13, 13, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 9, 9, 29, 29] 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]) total number of confs: 152 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360441551 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360441551 Building ZINC001360470645 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360470645 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/244 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccc(Br)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1C) `ZINC001360470645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360470645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360470645 none Cc1nn(c2ccc(Br)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', '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.2', '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, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 24, 24, 23, 24, 24, 24, 9, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 24, 24, 24, 24, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 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]) total number of confs: 57 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/245 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/245' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccc(Br)cc2)c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1C) `ZINC001360470645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360470645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360470645 none Cc1nn(c2ccc(Br)cc2)c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', '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.2', '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, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 24, 24, 24, 24, 24, 24, 9, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 24, 24, 24, 24, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 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]) total number of confs: 52 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360470645 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645 Building ZINC001360470645 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360470645 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 244) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(Br)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1C) `ZINC001360470645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360470645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360470645 none Cc1nn(c2ccc(Br)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', '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.2', '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, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 24, 24, 23, 24, 24, 24, 9, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 24, 24, 24, 24, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 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]) total number of confs: 57 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 245) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(Br)cc2)c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1C) `ZINC001360470645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360470645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360470645 none Cc1nn(c2ccc(Br)cc2)c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', '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.2', '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, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 24, 24, 24, 24, 24, 24, 9, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 24, 24, 24, 24, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 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]) total number of confs: 52 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360470645 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360470645 Building ZINC001360508144 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360508144 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/246 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001360508144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360508144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360508144 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](CC)CN1C(=O)OCc1ccccc1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 5, 8, 1, 11, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 3, 3, 3, 4, 3, 3, 3, 7, 7, 8, 32, 36, 36, 33, 36, 36, 3, 3, 3, 3, 3, 3, 3, 7, 7, 4, 4, 4, 4, 4, 3, 3, 32, 32, 36, 36, 36, 36, 36] 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, 54]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/247 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/247' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001360508144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360508144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360508144 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](CC)CN1C(=O)OCc1ccccc1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 5, 8, 1, 11, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 2, 2, 2, 3, 2, 2, 2, 4, 4, 7, 29, 36, 36, 33, 36, 36, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 2, 2, 29, 29, 36, 36, 36, 36, 36] 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, 54]) total number of confs: 140 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360508144 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144 Building ZINC001360508144 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360508144 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 246) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001360508144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360508144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360508144 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](CC)CN1C(=O)OCc1ccccc1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 5, 8, 1, 11, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 3, 3, 3, 4, 3, 3, 3, 7, 7, 8, 32, 36, 36, 33, 36, 36, 3, 3, 3, 3, 3, 3, 3, 7, 7, 4, 4, 4, 4, 4, 3, 3, 32, 32, 36, 36, 36, 36, 36] 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, 54]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 247) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001360508144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360508144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360508144 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](CC)CN1C(=O)OCc1ccccc1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 5, 8, 1, 11, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 2, 2, 2, 3, 2, 2, 2, 4, 4, 7, 29, 36, 36, 33, 36, 36, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 2, 2, 29, 29, 36, 36, 36, 36, 36] 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, 54]) total number of confs: 140 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360508144 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508144 Building ZINC001360508145 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360508145 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/248 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001360508145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360508145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360508145 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](CC)CN1C(=O)OCc1ccccc1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 5, 8, 1, 11, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 0 hydrogens need 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, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 2, 2, 2, 4, 4, 8, 30, 35, 35, 30, 35, 35, 3, 3, 3, 3, 3, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 30, 30, 35, 35, 30, 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, 54]) total number of confs: 139 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/249 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/249' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001360508145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360508145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360508145 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](CC)CN1C(=O)OCc1ccccc1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 5, 8, 1, 11, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 0 hydrogens 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, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 3, 3, 3, 4, 3, 3, 3, 5, 5, 7, 27, 34, 34, 27, 34, 34, 4, 4, 4, 4, 4, 3, 3, 5, 5, 4, 4, 4, 4, 4, 3, 3, 27, 27, 34, 34, 27, 34, 34] 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, 54]) total number of confs: 148 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360508145 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145 Building ZINC001360508145 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360508145 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 248) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001360508145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360508145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360508145 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](CC)CN1C(=O)OCc1ccccc1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 5, 8, 1, 11, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 0 hydrogens need 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, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 2, 2, 2, 4, 4, 8, 30, 35, 35, 30, 35, 35, 3, 3, 3, 3, 3, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 30, 30, 35, 35, 30, 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, 54]) total number of confs: 139 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 249) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001360508145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360508145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360508145 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@H](CC)CN1C(=O)OCc1ccccc1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 5, 8, 1, 11, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 0 hydrogens 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, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 3, 3, 3, 4, 3, 3, 3, 5, 5, 7, 27, 34, 34, 27, 34, 34, 4, 4, 4, 4, 4, 3, 3, 5, 5, 4, 4, 4, 4, 4, 3, 3, 27, 27, 34, 34, 27, 34, 34] 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, 54]) total number of confs: 148 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360508145 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508145 Building ZINC001360508146 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360508146 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/250 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001360508146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360508146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360508146 none CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](CC)CN1C(=O)OCc1ccccc1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 5, 8, 1, 11, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 0 hydrogens 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, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 4, 4, 4, 6, 6, 8, 29, 34, 34, 31, 34, 34, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 4, 4, 29, 29, 34, 34, 29, 34, 34] 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, 54]) total number of confs: 136 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/251 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001360508146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360508146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360508146 none CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](CC)CN1C(=O)OCc1ccccc1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 5, 8, 1, 11, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 0 hydrogens need 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, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 2, 2, 2, 3, 3, 7, 29, 35, 35, 29, 35, 35, 3, 3, 3, 3, 3, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 29, 29, 35, 35, 29, 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, 54]) total number of confs: 140 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360508146 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146 Building ZINC001360508146 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360508146 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 250) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001360508146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360508146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360508146 none CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](CC)CN1C(=O)OCc1ccccc1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 5, 8, 1, 11, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 0 hydrogens 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, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 4, 4, 4, 6, 6, 8, 29, 34, 34, 31, 34, 34, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 4, 4, 29, 29, 34, 34, 29, 34, 34] 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, 54]) total number of confs: 136 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 251) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001360508146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360508146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360508146 none CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[C@@H](CC)CN1C(=O)OCc1ccccc1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 5, 5, 5, 8, 1, 11, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 0 hydrogens need 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, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 2, 2, 2, 3, 3, 7, 29, 35, 35, 29, 35, 35, 3, 3, 3, 3, 3, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 29, 29, 35, 35, 29, 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, 54]) total number of confs: 140 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360508146 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508146 Building ZINC001360508147 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360508147 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/252 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)OCc2ccccc2)[C@@H](CC)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001360508147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360508147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001360508147 none CC[C@@H]1CN(C(=O)OCc2ccccc2)[C@@H](CC)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.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', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 9, 28, 38, 38, 28, 38, 38, 2, 2, 2, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 38, 38, 28, 38, 38, 4, 4, 4, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 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: 152 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/253 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/253' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)OCc2ccccc2)[C@@H](CC)CN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001360508147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360508147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001360508147 none CC[C@@H]1CN(C(=O)OCc2ccccc2)[C@@H](CC)CN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.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', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 7, 7, 9, 26, 34, 34, 26, 34, 34, 4, 4, 4, 6, 4, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 4, 4, 26, 26, 34, 34, 26, 34, 34, 6, 6, 6, 6, 6, 4, 4, 2, 2] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 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: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360508147 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147 Building ZINC001360508147 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360508147 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 252) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CN(C(=O)OCc2ccccc2)[C@@H](CC)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001360508147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360508147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001360508147 none CC[C@@H]1CN(C(=O)OCc2ccccc2)[C@@H](CC)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.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', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 9, 28, 38, 38, 28, 38, 38, 2, 2, 2, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 38, 38, 28, 38, 38, 4, 4, 4, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 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: 152 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 253) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/253: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CN(C(=O)OCc2ccccc2)[C@@H](CC)CN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001360508147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360508147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001360508147 none CC[C@@H]1CN(C(=O)OCc2ccccc2)[C@@H](CC)CN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.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', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 7, 7, 9, 26, 34, 34, 26, 34, 34, 4, 4, 4, 6, 4, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 4, 4, 26, 26, 34, 34, 26, 34, 34, 6, 6, 6, 6, 6, 4, 4, 2, 2] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 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: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360508147 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360508147 Building ZINC001360601177 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360601177 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/254 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)cc1OCC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360601177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360601177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC001360601177 none O=C(Nc1ccc(Cl)cc1OCC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 12, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 6, 10, 10, 10, 10, 24, 43, 43, 43, 43, 1, 1, 1, 8, 8, 8, 8, 8, 4, 10, 10, 10, 43, 43, 8, 8] 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/255 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/255' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)cc1OCC(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360601177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360601177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC001360601177 none O=C(Nc1ccc(Cl)cc1OCC(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 12, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 5, 10, 10, 10, 10, 23, 40, 40, 40, 40, 1, 1, 1, 8, 8, 8, 8, 8, 4, 10, 10, 10, 40, 40, 8, 8] 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360601177 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177 Building ZINC001360601177 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360601177 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 254) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1ccc(Cl)cc1OCC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360601177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360601177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC001360601177 none O=C(Nc1ccc(Cl)cc1OCC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 12, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 6, 10, 10, 10, 10, 24, 43, 43, 43, 43, 1, 1, 1, 8, 8, 8, 8, 8, 4, 10, 10, 10, 43, 43, 8, 8] 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 255) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1ccc(Cl)cc1OCC(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360601177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360601177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC001360601177 none O=C(Nc1ccc(Cl)cc1OCC(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 12, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 5, 10, 10, 10, 10, 23, 40, 40, 40, 40, 1, 1, 1, 8, 8, 8, 8, 8, 4, 10, 10, 10, 40, 40, 8, 8] 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360601177 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360601177 Building ZINC001360630852 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360630852 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/256 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(NC(=O)c2ccncc2)cc1) `ZINC001360630852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360630852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001360630852 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(NC(=O)c2ccncc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 15, 15, 10, 13, 37, 37, 37, 41, 41, 37, 41, 41, 15, 15, 8, 8, 8, 4, 3, 1, 3, 15, 15, 37, 41, 41, 41, 41, 15, 15] 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, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/257 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/257' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(NC(=O)c2ccncc2)cc1) `ZINC001360630852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360630852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001360630852 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(NC(=O)c2ccncc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 7, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 10, 10, 9, 10, 32, 32, 32, 39, 39, 32, 39, 39, 10, 10, 7, 7, 7, 4, 3, 1, 3, 10, 10, 32, 39, 39, 39, 39, 10, 10] 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, 44, 45, 46]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360630852 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852 Building ZINC001360630852 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360630852 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 256) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c1cc(Cl)cc(Cl)c1)c1ccc(NC(=O)c2ccncc2)cc1) `ZINC001360630852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360630852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001360630852 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(NC(=O)c2ccncc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 15, 15, 10, 13, 37, 37, 37, 41, 41, 37, 41, 41, 15, 15, 8, 8, 8, 4, 3, 1, 3, 15, 15, 37, 41, 41, 41, 41, 15, 15] 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, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 257) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/257: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c1cc(Cl)cc(Cl)c1)c1ccc(NC(=O)c2ccncc2)cc1) `ZINC001360630852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360630852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001360630852 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(NC(=O)c2ccncc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 7, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 10, 10, 9, 10, 32, 32, 32, 39, 39, 32, 39, 39, 10, 10, 7, 7, 7, 4, 3, 1, 3, 10, 10, 32, 39, 39, 39, 39, 10, 10] 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, 44, 45, 46]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360630852 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630852 Building ZINC001360630853 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360630853 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/258 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(NC(=O)c2ccncc2)cc1) `ZINC001360630853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360630853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001360630853 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(NC(=O)c2ccncc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 7, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 11, 11, 8, 8, 32, 32, 32, 40, 40, 32, 40, 40, 11, 11, 7, 7, 7, 4, 3, 1, 3, 11, 11, 32, 40, 40, 40, 40, 11, 11] 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, 44, 45, 46]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/259 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/259' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(NC(=O)c2ccncc2)cc1) `ZINC001360630853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360630853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001360630853 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(NC(=O)c2ccncc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 15, 15, 10, 11, 37, 37, 37, 41, 41, 40, 41, 41, 15, 15, 8, 8, 8, 4, 3, 1, 3, 15, 15, 37, 41, 41, 41, 41, 15, 15] 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, 44, 45, 46]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360630853 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853 Building ZINC001360630853 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360630853 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 258) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(NC(=O)c2ccncc2)cc1) `ZINC001360630853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360630853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001360630853 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(NC(=O)c2ccncc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 7, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 11, 11, 8, 8, 32, 32, 32, 40, 40, 32, 40, 40, 11, 11, 7, 7, 7, 4, 3, 1, 3, 11, 11, 32, 40, 40, 40, 40, 11, 11] 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, 44, 45, 46]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 259) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(NC(=O)c2ccncc2)cc1) `ZINC001360630853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360630853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001360630853 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(NC(=O)c2ccncc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 15, 15, 10, 11, 37, 37, 37, 41, 41, 40, 41, 41, 15, 15, 8, 8, 8, 4, 3, 1, 3, 15, 15, 37, 41, 41, 41, 41, 15, 15] 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, 44, 45, 46]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360630853 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360630853 Building ZINC001360680033 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360680033 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/260 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(c2cccc(Br)c2)cc1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001360680033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360680033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360680033 none CCOC(=O)c1sc(c2cccc(Br)c2)cc1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C 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', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 3, 7, 5, 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] 0 hydrogens 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, 11, 11, 4, 11, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 32, 32, 32, 32, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/261 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/261' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(c2cccc(Br)c2)cc1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001360680033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360680033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360680033 none CCOC(=O)c1sc(c2cccc(Br)c2)cc1NC(=O)[C@]([O-])([SiH3])C(C)(C)C 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', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 3, 7, 5, 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] 0 hydrogens 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, 11, 11, 4, 11, 4, 4, 4, 4, 33, 33, 13, 33, 33, 33, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 33, 33, 22, 33, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360680033 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033 Building ZINC001360680033 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360680033 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 260) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(Br)c2)cc1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001360680033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360680033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360680033 none CCOC(=O)c1sc(c2cccc(Br)c2)cc1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C 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', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 3, 7, 5, 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] 0 hydrogens 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, 11, 11, 4, 11, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 32, 32, 32, 32, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 261) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/261: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2cccc(Br)c2)cc1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001360680033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360680033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360680033 none CCOC(=O)c1sc(c2cccc(Br)c2)cc1NC(=O)[C@]([O-])([SiH3])C(C)(C)C 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', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 3, 7, 5, 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] 0 hydrogens 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, 11, 11, 4, 11, 4, 4, 4, 4, 33, 33, 13, 33, 33, 33, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 33, 33, 22, 33, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360680033 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360680033 Building ZINC001360780280 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360780280 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/262 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Br)cc2)CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001360780280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360780280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360780280 none O=C(NCC1(c2ccc(Br)cc2)CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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, 8, 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: [4, 1, 4, 4, 25, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 7, 7, 7, 7, 7, 4, 15, 15, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 7, 7] 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: 120 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/263 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/263' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Br)cc2)CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001360780280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360780280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360780280 none O=C(NCC1(c2ccc(Br)cc2)CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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, 8, 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, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 7, 7, 7, 7, 7, 3, 14, 14, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 7, 7] 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: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360780280 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280 Building ZINC001360780280 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360780280 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 262) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCC1(c2ccc(Br)cc2)CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001360780280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360780280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360780280 none O=C(NCC1(c2ccc(Br)cc2)CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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, 8, 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: [4, 1, 4, 4, 25, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 7, 7, 7, 7, 7, 4, 15, 15, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 7, 7] 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: 120 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 263) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCC1(c2ccc(Br)cc2)CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001360780280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360780280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360780280 none O=C(NCC1(c2ccc(Br)cc2)CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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, 8, 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, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 7, 7, 7, 7, 7, 3, 14, 14, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 7, 7] 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: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360780280 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360780280 Building ZINC001360782889 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360782889 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/264 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOCCN(C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)c1ccc(Br)cc1) `ZINC001360782889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360782889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001360782889 none CCCCOCCN(C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 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] 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] 0 hydrogens 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, 23, 11, 5, 4, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 41, 41, 41, 41, 41, 41, 41, 23, 23, 5, 5, 4, 4, 2, 2, 2, 2, 2, 2, 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, 48, 49]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/265 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/265' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOCCN(C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)c1ccc(Br)cc1) `ZINC001360782889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360782889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001360782889 none CCCCOCCN(C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 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] 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] 0 hydrogens 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, 30, 14, 7, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 30, 30, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2] 50 rigid atoms, others: [45, 43, 17, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 18, 19, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48, 49]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360782889 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889 Building ZINC001360782889 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360782889 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 264) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c1cc(F)ccc1C)c1ccc(Br)cc1) `ZINC001360782889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360782889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001360782889 none CCCCOCCN(C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 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] 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] 0 hydrogens 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, 23, 11, 5, 4, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 41, 41, 41, 41, 41, 41, 41, 23, 23, 5, 5, 4, 4, 2, 2, 2, 2, 2, 2, 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, 48, 49]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 265) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c1cc(F)ccc1C)c1ccc(Br)cc1) `ZINC001360782889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360782889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001360782889 none CCCCOCCN(C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 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] 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] 0 hydrogens 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, 30, 14, 7, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 30, 30, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2] 50 rigid atoms, others: [45, 43, 17, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 18, 19, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48, 49]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360782889 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360782889 Building ZINC001360828866 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360828866 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/266 `/scratch/xiaobo/182395/xbh-8058088.34/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)NCCc1cc(C)cc(C)c1) `ZINC001360828866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360828866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001360828866 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1cc(C)cc(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', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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'] dock atom type 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, 5, 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, 7] dock 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] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 2, 10, 10, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/267 `/scratch/xiaobo/182395/xbh-8058088.34/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)NCCc1cc(C)cc(C)c1) `ZINC001360828866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360828866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001360828866 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1cc(C)cc(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', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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'] dock atom type 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, 5, 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, 7] dock 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] 0 hydrogens need rotated 50 conformations in 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, 2, 9, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 9, 9, 13, 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, 55]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360828866 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866 Building ZINC001360828866 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360828866 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 266) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)NCCc1cc(C)cc(C)c1) `ZINC001360828866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360828866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001360828866 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1cc(C)cc(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', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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'] dock atom type 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, 5, 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, 7] dock 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] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 2, 10, 10, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 267) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)NCCc1cc(C)cc(C)c1) `ZINC001360828866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360828866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001360828866 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1cc(C)cc(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', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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'] dock atom type 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, 5, 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, 7] dock 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] 0 hydrogens need rotated 50 conformations in 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, 2, 9, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 9, 9, 13, 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, 55]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360828866 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360828866 Building ZINC001360866809 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360866809 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/268 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3cc(Br)ccc3n2Cc2ccccc2)cc1) `ZINC001360866809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360866809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360866809 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3cc(Br)ccc3n2Cc2ccccc2)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 17, 1, 1, 1, 8, 5, 1, 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] 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] 0 hydrogens 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, 5, 5, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 33, 50, 50, 39, 50, 50, 5, 5, 5, 5, 5, 5, 5, 4, 8, 8, 8, 33, 33, 50, 50, 50, 50, 50, 5, 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]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/269 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3cc(Br)ccc3n2Cc2ccccc2)cc1) `ZINC001360866809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360866809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360866809 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3cc(Br)ccc3n2Cc2ccccc2)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 17, 1, 1, 1, 8, 5, 1, 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] 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] 0 hydrogens 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, 5, 5, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 34, 50, 50, 41, 50, 50, 5, 5, 5, 5, 5, 5, 5, 4, 8, 8, 8, 34, 34, 50, 50, 50, 50, 50, 5, 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]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360866809 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809 Building ZINC001360866809 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360866809 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 268) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3cc(Br)ccc3n2Cc2ccccc2)cc1) `ZINC001360866809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360866809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360866809 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3cc(Br)ccc3n2Cc2ccccc2)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 17, 1, 1, 1, 8, 5, 1, 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] 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] 0 hydrogens 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, 5, 5, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 33, 50, 50, 39, 50, 50, 5, 5, 5, 5, 5, 5, 5, 4, 8, 8, 8, 33, 33, 50, 50, 50, 50, 50, 5, 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]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 269) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3cc(Br)ccc3n2Cc2ccccc2)cc1) `ZINC001360866809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360866809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360866809 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3cc(Br)ccc3n2Cc2ccccc2)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 17, 1, 1, 1, 8, 5, 1, 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] 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] 0 hydrogens 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, 5, 5, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 34, 50, 50, 41, 50, 50, 5, 5, 5, 5, 5, 5, 5, 4, 8, 8, 8, 34, 34, 50, 50, 50, 50, 50, 5, 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]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360866809 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360866809 Building ZINC001360867335 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360867335 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/270 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2nc3cc(Br)ccc3n2Cc2ccccc2)c1) `ZINC001360867335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360867335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001360867335 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2nc3cc(Br)ccc3n2Cc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 17, 1, 1, 1, 8, 5, 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] 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] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 27, 27, 25, 27, 27, 6, 6, 6, 6, 2, 6, 6, 2, 6, 6, 6, 20, 20, 27, 27, 27, 27, 27, 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, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/271 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/271' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2nc3cc(Br)ccc3n2Cc2ccccc2)c1) `ZINC001360867335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360867335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001360867335 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2nc3cc(Br)ccc3n2Cc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 17, 1, 1, 1, 8, 5, 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] 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] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 27, 27, 26, 27, 27, 6, 6, 6, 6, 6, 6, 6, 2, 6, 6, 6, 20, 20, 27, 27, 27, 27, 27, 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, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360867335 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335 Building ZINC001360867335 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360867335 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 270) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2nc3cc(Br)ccc3n2Cc2ccccc2)c1) `ZINC001360867335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360867335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001360867335 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2nc3cc(Br)ccc3n2Cc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 17, 1, 1, 1, 8, 5, 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] 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] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 27, 27, 25, 27, 27, 6, 6, 6, 6, 2, 6, 6, 2, 6, 6, 6, 20, 20, 27, 27, 27, 27, 27, 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, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 271) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2nc3cc(Br)ccc3n2Cc2ccccc2)c1) `ZINC001360867335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360867335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001360867335 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2nc3cc(Br)ccc3n2Cc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 17, 1, 1, 1, 8, 5, 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] 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] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 27, 27, 26, 27, 27, 6, 6, 6, 6, 6, 6, 6, 2, 6, 6, 6, 20, 20, 27, 27, 27, 27, 27, 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, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360867335 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360867335 Building ZINC001360897051 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360897051 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/272 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H](Cc1ccc(F)cc1)C(C)C) `ZINC001360897051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360897051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360897051 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H](Cc1ccc(F)cc1)C(C)C 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.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 1, 1, 1, 1, 15, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 8, 17, 17, 24, 27, 27, 24, 24, 27, 27, 17, 19, 19, 9, 9, 9, 9, 9, 7, 7, 24, 24, 27, 27, 27, 27, 19, 19, 19, 19, 19, 19, 19] 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]) total number of confs: 144 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/273 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H](Cc1ccc(F)cc1)C(C)C) `ZINC001360897051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360897051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360897051 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H](Cc1ccc(F)cc1)C(C)C 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.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 1, 1, 1, 1, 15, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 15, 15, 24, 26, 26, 24, 26, 26, 26, 15, 20, 20, 7, 7, 7, 7, 7, 7, 7, 24, 24, 26, 26, 26, 26, 20, 20, 20, 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]) total number of confs: 148 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360897051 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051 Building ZINC001360897051 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360897051 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 272) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/272: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c1ccc(Br)s1)[C@@H](Cc1ccc(F)cc1)C(C)C) `ZINC001360897051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360897051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360897051 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H](Cc1ccc(F)cc1)C(C)C 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.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 1, 1, 1, 1, 15, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 8, 17, 17, 24, 27, 27, 24, 24, 27, 27, 17, 19, 19, 9, 9, 9, 9, 9, 7, 7, 24, 24, 27, 27, 27, 27, 19, 19, 19, 19, 19, 19, 19] 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]) total number of confs: 144 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 273) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/273: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c1ccc(Br)s1)[C@@H](Cc1ccc(F)cc1)C(C)C) `ZINC001360897051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360897051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360897051 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H](Cc1ccc(F)cc1)C(C)C 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.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 1, 1, 1, 1, 15, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 15, 15, 24, 26, 26, 24, 26, 26, 26, 15, 20, 20, 7, 7, 7, 7, 7, 7, 7, 24, 24, 26, 26, 26, 26, 20, 20, 20, 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]) total number of confs: 148 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360897051 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897051 Building ZINC001360897052 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360897052 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/274 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H](Cc1ccc(F)cc1)C(C)C) `ZINC001360897052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360897052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360897052 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H](Cc1ccc(F)cc1)C(C)C 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.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 1, 1, 1, 1, 15, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 17, 17, 26, 28, 28, 26, 28, 28, 28, 17, 22, 22, 8, 8, 8, 8, 8, 6, 6, 26, 26, 28, 28, 28, 28, 22, 22, 22, 22, 22, 22, 22] 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]) total number of confs: 158 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/275 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/275' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H](Cc1ccc(F)cc1)C(C)C) `ZINC001360897052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360897052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360897052 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H](Cc1ccc(F)cc1)C(C)C 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.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 1, 1, 1, 1, 15, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 8, 17, 17, 24, 27, 27, 24, 27, 27, 27, 17, 19, 19, 9, 9, 9, 9, 9, 7, 7, 24, 24, 27, 27, 27, 27, 19, 19, 19, 19, 19, 19, 19] 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]) total number of confs: 150 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360897052 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052 Building ZINC001360897052 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360897052 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 274) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H](Cc1ccc(F)cc1)C(C)C) `ZINC001360897052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360897052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360897052 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H](Cc1ccc(F)cc1)C(C)C 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.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 1, 1, 1, 1, 15, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 17, 17, 26, 28, 28, 26, 28, 28, 28, 17, 22, 22, 8, 8, 8, 8, 8, 6, 6, 26, 26, 28, 28, 28, 28, 22, 22, 22, 22, 22, 22, 22] 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]) total number of confs: 158 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 275) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H](Cc1ccc(F)cc1)C(C)C) `ZINC001360897052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360897052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360897052 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H](Cc1ccc(F)cc1)C(C)C 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.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 1, 1, 1, 1, 15, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 8, 17, 17, 24, 27, 27, 24, 27, 27, 27, 17, 19, 19, 9, 9, 9, 9, 9, 7, 7, 24, 24, 27, 27, 27, 27, 19, 19, 19, 19, 19, 19, 19] 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]) total number of confs: 150 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360897052 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360897052 Building ZINC001360914210 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360914210 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/276 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(SC)cc1OC) `ZINC001360914210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360914210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360914210 none COc1cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(SC)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 14, 5, 1, 1, 12, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 18, 18, 18, 13, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 18, 18, 27, 18, 18, 18, 32, 34, 34, 34, 18, 13, 13, 5, 5, 5, 2, 1, 2, 27, 27, 27, 18, 32, 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, 44, 45]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/277 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/277' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CN(C)C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(SC)cc1OC) `ZINC001360914210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360914210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360914210 none COc1cc(CN(C)C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(SC)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 14, 5, 1, 1, 12, 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, 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] 0 hydrogens 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, 18, 18, 18, 13, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 18, 18, 27, 18, 18, 18, 30, 33, 33, 33, 18, 13, 13, 5, 5, 5, 2, 1, 2, 27, 27, 27, 18, 30, 30, 30] 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: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360914210 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210 Building ZINC001360914210 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360914210 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 276) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(SC)cc1OC) `ZINC001360914210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360914210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360914210 none COc1cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(SC)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 14, 5, 1, 1, 12, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 18, 18, 18, 13, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 18, 18, 27, 18, 18, 18, 32, 34, 34, 34, 18, 13, 13, 5, 5, 5, 2, 1, 2, 27, 27, 27, 18, 32, 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, 44, 45]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 277) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1cc(CN(C)C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(SC)cc1OC) `ZINC001360914210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360914210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001360914210 none COc1cc(CN(C)C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(SC)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 14, 5, 1, 1, 12, 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, 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] 0 hydrogens 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, 18, 18, 18, 13, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 18, 18, 27, 18, 18, 18, 30, 33, 33, 33, 18, 13, 13, 5, 5, 5, 2, 1, 2, 27, 27, 27, 18, 30, 30, 30] 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: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360914210 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360914210 Building ZINC001360983002 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360983002 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/278 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2ccccc2n1c1ccccc1F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360983002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360983002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001360983002 none O=C(Nc1nc2ccccc2n1c1ccccc1F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 7, 26, 26, 26, 1, 1, 1, 10, 10, 10, 10, 10, 3, 7, 7, 7, 7, 26, 26, 26, 26, 10, 10] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/279 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/279' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2ccccc2n1c1ccccc1F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360983002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360983002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001360983002 none O=C(Nc1nc2ccccc2n1c1ccccc1F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 1, 1, 1, 10, 10, 10, 10, 10, 3, 7, 7, 7, 7, 26, 26, 26, 26, 10, 10] 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]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360983002 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002 Building ZINC001360983002 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360983002 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 278) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1nc2ccccc2n1c1ccccc1F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360983002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360983002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001360983002 none O=C(Nc1nc2ccccc2n1c1ccccc1F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 7, 26, 26, 26, 1, 1, 1, 10, 10, 10, 10, 10, 3, 7, 7, 7, 7, 26, 26, 26, 26, 10, 10] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 279) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1nc2ccccc2n1c1ccccc1F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001360983002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360983002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001360983002 none O=C(Nc1nc2ccccc2n1c1ccccc1F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 1, 1, 1, 10, 10, 10, 10, 10, 3, 7, 7, 7, 7, 26, 26, 26, 26, 10, 10] 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]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001360983002 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001360983002 Building ZINC001361033399 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361033399 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/280 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001361033399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361033399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361033399 none O=C(N[C@@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', '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, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [4, 1, 4, 4, 8, 8, 45, 45, 45, 45, 45, 45, 45, 45, 45, 8, 21, 21, 9, 21, 21, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 45, 45, 45, 45, 45, 45, 45, 21, 21, 9, 21, 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]) total number of confs: 131 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/281 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/281' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001361033399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361033399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361033399 none O=C(N[C@@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', '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, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [5, 1, 5, 5, 9, 9, 49, 49, 49, 49, 49, 49, 49, 49, 49, 9, 17, 17, 9, 17, 17, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 49, 49, 49, 49, 49, 49, 49, 17, 17, 9, 17, 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]) total number of confs: 122 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361033399 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399 Building ZINC001361033399 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361033399 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 280) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001361033399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361033399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361033399 none O=C(N[C@@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', '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, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [4, 1, 4, 4, 8, 8, 45, 45, 45, 45, 45, 45, 45, 45, 45, 8, 21, 21, 9, 21, 21, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 45, 45, 45, 45, 45, 45, 45, 21, 21, 9, 21, 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]) total number of confs: 131 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 281) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001361033399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361033399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361033399 none O=C(N[C@@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', '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, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [5, 1, 5, 5, 9, 9, 49, 49, 49, 49, 49, 49, 49, 49, 49, 9, 17, 17, 9, 17, 17, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 49, 49, 49, 49, 49, 49, 49, 17, 17, 9, 17, 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]) total number of confs: 122 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361033399 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033399 Building ZINC001361033400 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361033400 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/282 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001361033400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361033400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361033400 none O=C(N[C@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', '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, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [5, 1, 5, 5, 9, 9, 48, 48, 48, 48, 48, 48, 48, 48, 48, 9, 17, 17, 9, 17, 17, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 48, 48, 48, 48, 48, 48, 48, 17, 17, 17, 17, 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]) total number of confs: 133 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/283 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/283' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001361033400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361033400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361033400 none O=C(N[C@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', '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, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [4, 1, 4, 4, 8, 8, 48, 48, 48, 48, 48, 48, 48, 48, 48, 8, 17, 17, 8, 17, 17, 17, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 48, 48, 48, 48, 48, 48, 48, 17, 17, 9, 17, 3, 3, 3, 3] 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]) total number of confs: 126 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361033400 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400 Building ZINC001361033400 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361033400 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 282) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001361033400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361033400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361033400 none O=C(N[C@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', '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, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [5, 1, 5, 5, 9, 9, 48, 48, 48, 48, 48, 48, 48, 48, 48, 9, 17, 17, 9, 17, 17, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 48, 48, 48, 48, 48, 48, 48, 17, 17, 17, 17, 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]) total number of confs: 133 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 283) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001361033400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361033400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361033400 none O=C(N[C@H](c1ccc2c(c1)OCCO2)c1ccccc1Cl)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', '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, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [4, 1, 4, 4, 8, 8, 48, 48, 48, 48, 48, 48, 48, 48, 48, 8, 17, 17, 8, 17, 17, 17, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 48, 48, 48, 48, 48, 48, 48, 17, 17, 9, 17, 3, 3, 3, 3] 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]) total number of confs: 126 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361033400 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361033400 Building ZINC001361086123 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361086123 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/284 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2c(F)cccc2F)CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001361086123.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361086123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001361086123 none O=C(NCC1(c2c(F)cccc2F)CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 15, 1, 1, 1, 1, 15, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens 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, 16, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 8, 8, 8, 8, 8, 4, 12, 12, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 8, 8] 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]) total number of confs: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/285 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/285' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2c(F)cccc2F)CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001361086123.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361086123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001361086123 none O=C(NCC1(c2c(F)cccc2F)CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 15, 1, 1, 1, 1, 15, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 14, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 7, 7, 7, 7, 7, 3, 12, 12, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 7, 7] 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]) total number of confs: 114 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361086123 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123 Building ZINC001361086123 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361086123 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 284) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCC1(c2c(F)cccc2F)CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001361086123.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361086123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001361086123 none O=C(NCC1(c2c(F)cccc2F)CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 15, 1, 1, 1, 1, 15, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens 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, 16, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 8, 8, 8, 8, 8, 4, 12, 12, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 8, 8] 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]) total number of confs: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 285) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCC1(c2c(F)cccc2F)CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001361086123.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361086123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001361086123 none O=C(NCC1(c2c(F)cccc2F)CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 15, 1, 1, 1, 1, 15, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 14, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 7, 7, 7, 7, 7, 3, 12, 12, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 7, 7] 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]) total number of confs: 114 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361086123 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361086123 Building ZINC001361089043 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361089043 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/286 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2ccc(F)cc2)cc1) `ZINC001361089043.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361089043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361089043 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2ccc(F)cc2)cc1 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', 'Br', 'S.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 28, 28, 8, 4, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 18, 18, 8, 8, 18, 18, 28, 28, 28, 28, 28, 28, 28, 4, 8, 8, 18, 18, 18, 18, 28, 28] 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: 156 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/287 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2ccc(F)cc2)cc1) `ZINC001361089043.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361089043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361089043 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2ccc(F)cc2)cc1 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', 'Br', 'S.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 28, 28, 7, 4, 7, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 7, 16, 16, 7, 7, 16, 16, 28, 28, 28, 28, 28, 28, 28, 4, 8, 8, 16, 16, 16, 16, 28, 28] 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: 155 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361089043 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043 Building ZINC001361089043 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361089043 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 286) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2ccc(F)cc2)cc1) `ZINC001361089043.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361089043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361089043 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2ccc(F)cc2)cc1 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', 'Br', 'S.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 28, 28, 8, 4, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 18, 18, 8, 8, 18, 18, 28, 28, 28, 28, 28, 28, 28, 4, 8, 8, 18, 18, 18, 18, 28, 28] 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: 156 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 287) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2ccc(F)cc2)cc1) `ZINC001361089043.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361089043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361089043 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2ccc(F)cc2)cc1 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', 'Br', 'S.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 28, 28, 7, 4, 7, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 7, 16, 16, 7, 7, 16, 16, 28, 28, 28, 28, 28, 28, 28, 4, 8, 8, 16, 16, 16, 16, 28, 28] 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: 155 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361089043 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089043 Building ZINC001361089044 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361089044 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/288 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2ccc(F)cc2)cc1) `ZINC001361089044.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361089044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361089044 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2ccc(F)cc2)cc1 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', 'Br', 'S.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 30, 30, 7, 4, 7, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 7, 15, 15, 7, 7, 15, 15, 30, 30, 30, 30, 30, 30, 30, 4, 8, 8, 15, 15, 15, 15, 30, 30] 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: 156 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/289 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2ccc(F)cc2)cc1) `ZINC001361089044.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361089044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361089044 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2ccc(F)cc2)cc1 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', 'Br', 'S.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 8, 29, 29, 8, 4, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 18, 18, 8, 8, 18, 18, 29, 29, 29, 29, 29, 29, 29, 4, 8, 8, 18, 18, 18, 18, 29, 29] 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: 167 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361089044 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044 Building ZINC001361089044 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361089044 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 288) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2ccc(F)cc2)cc1) `ZINC001361089044.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361089044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361089044 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2ccc(F)cc2)cc1 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', 'Br', 'S.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 30, 30, 7, 4, 7, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 7, 15, 15, 7, 7, 15, 15, 30, 30, 30, 30, 30, 30, 30, 4, 8, 8, 15, 15, 15, 15, 30, 30] 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: 156 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 289) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2ccc(F)cc2)cc1) `ZINC001361089044.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361089044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361089044 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2ccc(F)cc2)cc1 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', 'Br', 'S.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 8, 29, 29, 8, 4, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 18, 18, 8, 8, 18, 18, 29, 29, 29, 29, 29, 29, 29, 4, 8, 8, 18, 18, 18, 18, 29, 29] 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: 167 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361089044 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361089044 Building ZINC001361119070 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001361119070 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/290 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCOc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1) `ZINC001361119070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361119070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001361119070 none CN(CCCOc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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.2', 'C.2', 'Cl', 'S.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, 10, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 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, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 44, 39, 24, 14, 14, 14, 14, 14, 14, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 47, 47, 45, 45, 39, 39, 14, 14, 14, 14, 9, 9, 2, 4, 4, 48, 48, 48, 48, 48, 48, 48, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/291 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/291' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCOc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1) `ZINC001361119070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361119070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001361119070 none CN(CCCOc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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.2', 'C.2', 'Cl', 'S.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, 10, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 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, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 44, 39, 24, 14, 14, 14, 14, 14, 14, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 47, 47, 45, 45, 39, 39, 14, 14, 14, 14, 9, 9, 2, 4, 4, 48, 48, 48, 48, 48, 48, 48, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/292 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/292' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCOc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1) `ZINC001361119070.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001361119070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/2/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'} 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 59 natoms 58 natoms 57 natoms 56 names: ZINC001361119070 none CN(CCCOc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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.2', 'C.2', 'Cl', 'S.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, 10, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 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, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 44, 40, 26, 16, 16, 16, 16, 16, 16, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 45, 45, 40, 40, 16, 16, 16, 16, 9, 9, 2, 4, 4, 48, 48, 48, 48, 48, 48, 48, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/293 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/293' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCOc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1) `ZINC001361119070.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001361119070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/3/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'} 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 59 natoms 58 natoms 57 natoms 56 names: ZINC001361119070 none CN(CCCOc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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.2', 'C.2', 'Cl', 'S.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, 10, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 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, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 44, 40, 26, 16, 16, 16, 16, 16, 16, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 45, 45, 40, 40, 16, 16, 16, 16, 9, 9, 2, 4, 4, 48, 48, 48, 48, 48, 48, 48, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361119070 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 Building ZINC001361119070 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001361119070 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 290) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(CCCOc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1) `ZINC001361119070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361119070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001361119070 none CN(CCCOc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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.2', 'C.2', 'Cl', 'S.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, 10, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 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, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 44, 39, 24, 14, 14, 14, 14, 14, 14, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 47, 47, 45, 45, 39, 39, 14, 14, 14, 14, 9, 9, 2, 4, 4, 48, 48, 48, 48, 48, 48, 48, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 291) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(CCCOc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1) `ZINC001361119070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361119070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001361119070 none CN(CCCOc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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.2', 'C.2', 'Cl', 'S.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, 10, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 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, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 44, 39, 24, 14, 14, 14, 14, 14, 14, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 47, 47, 45, 45, 39, 39, 14, 14, 14, 14, 9, 9, 2, 4, 4, 48, 48, 48, 48, 48, 48, 48, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 292) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/292: 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(CCCOc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1) `ZINC001361119070.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001361119070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/2/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'} 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 59 natoms 58 natoms 57 natoms 56 names: ZINC001361119070 none CN(CCCOc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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.2', 'C.2', 'Cl', 'S.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, 10, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 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, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 44, 40, 26, 16, 16, 16, 16, 16, 16, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 45, 45, 40, 40, 16, 16, 16, 16, 9, 9, 2, 4, 4, 48, 48, 48, 48, 48, 48, 48, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 293) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/293: 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(CCCOc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1) `ZINC001361119070.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001361119070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/3/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'} 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 59 natoms 58 natoms 57 natoms 56 names: ZINC001361119070 none CN(CCCOc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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.2', 'C.2', 'Cl', 'S.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, 10, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 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, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 44, 40, 26, 16, 16, 16, 16, 16, 16, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 45, 45, 40, 40, 16, 16, 16, 16, 9, 9, 2, 4, 4, 48, 48, 48, 48, 48, 48, 48, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361119070 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 Building ZINC001361119070 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001361119070 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 290) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(CCCOc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1) `ZINC001361119070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361119070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001361119070 none CN(CCCOc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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.2', 'C.2', 'Cl', 'S.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, 10, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 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, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 44, 39, 24, 14, 14, 14, 14, 14, 14, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 47, 47, 45, 45, 39, 39, 14, 14, 14, 14, 9, 9, 2, 4, 4, 48, 48, 48, 48, 48, 48, 48, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 291) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(CCCOc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1) `ZINC001361119070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361119070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001361119070 none CN(CCCOc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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.2', 'C.2', 'Cl', 'S.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, 10, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 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, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 44, 39, 24, 14, 14, 14, 14, 14, 14, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 47, 47, 45, 45, 39, 39, 14, 14, 14, 14, 9, 9, 2, 4, 4, 48, 48, 48, 48, 48, 48, 48, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 292) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/292: 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(CCCOc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1) `ZINC001361119070.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001361119070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/2/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'} 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 59 natoms 58 natoms 57 natoms 56 names: ZINC001361119070 none CN(CCCOc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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.2', 'C.2', 'Cl', 'S.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, 10, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 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, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 44, 40, 26, 16, 16, 16, 16, 16, 16, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 45, 45, 40, 40, 16, 16, 16, 16, 9, 9, 2, 4, 4, 48, 48, 48, 48, 48, 48, 48, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 293) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/293: 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(CCCOc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1) `ZINC001361119070.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001361119070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/3/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'} 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 59 natoms 58 natoms 57 natoms 56 names: ZINC001361119070 none CN(CCCOc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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.2', 'C.2', 'Cl', 'S.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, 10, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 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, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 44, 40, 26, 16, 16, 16, 16, 16, 16, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 45, 45, 40, 40, 16, 16, 16, 16, 9, 9, 2, 4, 4, 48, 48, 48, 48, 48, 48, 48, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361119070 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 Building ZINC001361119070 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001361119070 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 290) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(CCCOc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1) `ZINC001361119070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361119070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001361119070 none CN(CCCOc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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.2', 'C.2', 'Cl', 'S.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, 10, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 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, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 44, 39, 24, 14, 14, 14, 14, 14, 14, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 47, 47, 45, 45, 39, 39, 14, 14, 14, 14, 9, 9, 2, 4, 4, 48, 48, 48, 48, 48, 48, 48, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 291) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(CCCOc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1) `ZINC001361119070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361119070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001361119070 none CN(CCCOc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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.2', 'C.2', 'Cl', 'S.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, 10, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 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, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 44, 39, 24, 14, 14, 14, 14, 14, 14, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 47, 47, 45, 45, 39, 39, 14, 14, 14, 14, 9, 9, 2, 4, 4, 48, 48, 48, 48, 48, 48, 48, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 292) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/292: 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(CCCOc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1) `ZINC001361119070.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001361119070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/2/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'} 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 59 natoms 58 natoms 57 natoms 56 names: ZINC001361119070 none CN(CCCOc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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.2', 'C.2', 'Cl', 'S.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, 10, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 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, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 44, 40, 26, 16, 16, 16, 16, 16, 16, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 45, 45, 40, 40, 16, 16, 16, 16, 9, 9, 2, 4, 4, 48, 48, 48, 48, 48, 48, 48, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 293) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/293: 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(CCCOc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1) `ZINC001361119070.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001361119070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/3/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'} 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 59 natoms 58 natoms 57 natoms 56 names: ZINC001361119070 none CN(CCCOc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.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.2', 'C.2', 'Cl', 'S.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, 10, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 5, 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, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 44, 40, 26, 16, 16, 16, 16, 16, 16, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 45, 45, 40, 40, 16, 16, 16, 16, 9, 9, 2, 4, 4, 48, 48, 48, 48, 48, 48, 48, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361119070 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361119070 Building ZINC001361130324 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361130324 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/294 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc2C1) `ZINC001361130324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361130324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001361130324 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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: [50, 50, 50, 50, 29, 14, 29, 14, 14, 14, 9, 3, 10, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 14, 14, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 2, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/295 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/295' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc2C1) `ZINC001361130324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361130324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001361130324 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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: [50, 50, 50, 50, 30, 14, 30, 14, 14, 14, 9, 3, 10, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 14, 14, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 2, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361130324 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324 Building ZINC001361130324 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361130324 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 294) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc2C1) `ZINC001361130324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361130324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001361130324 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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: [50, 50, 50, 50, 29, 14, 29, 14, 14, 14, 9, 3, 10, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 14, 14, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 2, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 295) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc2C1) `ZINC001361130324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361130324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001361130324 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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: [50, 50, 50, 50, 30, 14, 30, 14, 14, 14, 9, 3, 10, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 14, 14, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 2, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361130324 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361130324 Building ZINC001361132911 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361132911 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/296 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3nc4cc(F)ccc4n3C(C)C)ccc2C)cn1) `ZINC001361132911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361132911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361132911 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3nc4cc(F)ccc4n3C(C)C)ccc2C)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', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 7, 7, 12, 12, 12, 12, 12, 7, 4, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 11, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/297 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/297' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(c3nc4cc(F)ccc4n3C(C)C)ccc2C)cn1) `ZINC001361132911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361132911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361132911 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(c3nc4cc(F)ccc4n3C(C)C)ccc2C)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', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 10, 10, 7, 7, 11, 11, 11, 11, 11, 7, 4, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 10, 10, 10, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361132911 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911 Building ZINC001361132911 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361132911 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 296) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3nc4cc(F)ccc4n3C(C)C)ccc2C)cn1) `ZINC001361132911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361132911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361132911 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3nc4cc(F)ccc4n3C(C)C)ccc2C)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', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 7, 7, 12, 12, 12, 12, 12, 7, 4, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 11, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 297) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(c3nc4cc(F)ccc4n3C(C)C)ccc2C)cn1) `ZINC001361132911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361132911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361132911 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(c3nc4cc(F)ccc4n3C(C)C)ccc2C)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', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 10, 10, 7, 7, 11, 11, 11, 11, 11, 7, 4, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 10, 10, 10, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361132911 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361132911 Building ZINC001361168654 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361168654 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/298 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Sc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)cc1) `ZINC001361168654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361168654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001361168654 none COc1ccc(Sc2ccc(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', 'S.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', '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, 14, 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, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 37, 37, 25, 4, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 37, 37, 37, 37, 37, 37, 37, 8, 8, 2, 5, 5, 5, 5, 5, 5, 5, 8, 8, 37, 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, 47, 48, 49]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/299 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/299' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Sc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)cc1) `ZINC001361168654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361168654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001361168654 none COc1ccc(Sc2ccc(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', 'S.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', '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, 14, 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, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 34, 37, 37, 21, 2, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 37, 37, 37, 37, 37, 37, 37, 8, 8, 2, 5, 5, 5, 5, 5, 5, 5, 8, 8, 37, 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, 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/182395/xbh-8058088.34/working/building/ZINC001361168654 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361168654 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654 Building ZINC001361168654 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361168654 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 298) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc(Sc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)cc1) `ZINC001361168654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361168654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001361168654 none COc1ccc(Sc2ccc(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', 'S.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', '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, 14, 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, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 37, 37, 25, 4, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 37, 37, 37, 37, 37, 37, 37, 8, 8, 2, 5, 5, 5, 5, 5, 5, 5, 8, 8, 37, 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, 47, 48, 49]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 299) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc(Sc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)cc1) `ZINC001361168654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361168654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001361168654 none COc1ccc(Sc2ccc(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', 'S.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', '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, 14, 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, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 34, 37, 37, 21, 2, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 37, 37, 37, 37, 37, 37, 37, 8, 8, 2, 5, 5, 5, 5, 5, 5, 5, 8, 8, 37, 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, 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/182395/xbh-8058088.34/working/building/ZINC001361168654 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361168654 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361168654 Building ZINC001361222283 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361222283 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/300 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2ccccc2n1CCc1ccccn1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001361222283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361222283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361222283 none O=C(Nc1nc2ccccc2n1CCc1ccccn1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 8, 10, 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: [3, 1, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 22, 37, 37, 37, 37, 37, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 3, 7, 7, 7, 7, 13, 13, 22, 22, 37, 37, 37, 37, 5, 2, 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/301 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/301' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2ccccc2n1CCc1ccccn1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001361222283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361222283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361222283 none O=C(Nc1nc2ccccc2n1CCc1ccccn1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 8, 10, 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: [3, 1, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 21, 36, 36, 36, 36, 36, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 3, 7, 7, 7, 7, 13, 13, 21, 21, 36, 36, 36, 36, 5, 1, 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361222283 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283 Building ZINC001361222283 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361222283 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 300) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1nc2ccccc2n1CCc1ccccn1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001361222283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361222283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361222283 none O=C(Nc1nc2ccccc2n1CCc1ccccn1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 8, 10, 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: [3, 1, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 22, 37, 37, 37, 37, 37, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 3, 7, 7, 7, 7, 13, 13, 22, 22, 37, 37, 37, 37, 5, 2, 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 301) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1nc2ccccc2n1CCc1ccccn1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001361222283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361222283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361222283 none O=C(Nc1nc2ccccc2n1CCc1ccccn1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 8, 10, 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: [3, 1, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 21, 36, 36, 36, 36, 36, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 3, 7, 7, 7, 7, 13, 13, 21, 21, 36, 36, 36, 36, 5, 1, 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361222283 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361222283 Building ZINC001361244041 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361244041 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/302 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2Cl)c(OC)c1) `ZINC001361244041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361244041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361244041 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)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.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', '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, 1, 1, 1, 1, 5, 5, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 8, 13, 13, 8, 4, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 12, 12, 8, 12, 12, 12, 13, 13, 19, 13, 20, 20, 20, 13, 13, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 8, 12, 19, 19, 19, 13] 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: 113 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/303 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/303' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2Cl)c(OC)c1) `ZINC001361244041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361244041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361244041 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)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.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', '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, 1, 1, 1, 1, 5, 5, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 7, 14, 14, 7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 13, 13, 7, 13, 13, 13, 14, 14, 18, 14, 23, 23, 23, 14, 14, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 7, 13, 18, 18, 18, 14] 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: 131 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361244041 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041 Building ZINC001361244041 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361244041 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 302) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2Cl)c(OC)c1) `ZINC001361244041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361244041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361244041 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)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.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', '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, 1, 1, 1, 1, 5, 5, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 8, 13, 13, 8, 4, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 12, 12, 8, 12, 12, 12, 13, 13, 19, 13, 20, 20, 20, 13, 13, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 8, 12, 19, 19, 19, 13] 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: 113 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 303) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2Cl)c(OC)c1) `ZINC001361244041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361244041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361244041 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)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.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', '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, 1, 1, 1, 1, 5, 5, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 7, 14, 14, 7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 13, 13, 7, 13, 13, 13, 14, 14, 18, 14, 23, 23, 23, 14, 14, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 7, 13, 18, 18, 18, 14] 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: 131 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361244041 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244041 Building ZINC001361244042 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361244042 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/304 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2Cl)c(OC)c1) `ZINC001361244042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361244042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361244042 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)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.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', '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, 1, 1, 1, 1, 5, 5, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 7, 14, 14, 7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 13, 13, 7, 13, 13, 13, 14, 14, 18, 14, 22, 22, 22, 14, 14, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 7, 13, 18, 18, 18, 14] 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: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/305 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2Cl)c(OC)c1) `ZINC001361244042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361244042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361244042 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)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.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', '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, 1, 1, 1, 1, 5, 5, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 8, 13, 13, 8, 4, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 12, 12, 8, 12, 12, 12, 13, 13, 19, 13, 20, 20, 20, 13, 13, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 8, 12, 19, 19, 19, 13] 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: 113 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361244042 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042 Building ZINC001361244042 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361244042 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 304) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2Cl)c(OC)c1) `ZINC001361244042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361244042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361244042 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)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.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', '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, 1, 1, 1, 1, 5, 5, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 7, 14, 14, 7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 13, 13, 7, 13, 13, 13, 14, 14, 18, 14, 22, 22, 22, 14, 14, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 7, 13, 18, 18, 18, 14] 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: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 305) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2Cl)c(OC)c1) `ZINC001361244042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361244042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001361244042 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)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.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', '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, 1, 1, 1, 1, 5, 5, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 8, 13, 13, 8, 4, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 12, 12, 8, 12, 12, 12, 13, 13, 19, 13, 20, 20, 20, 13, 13, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 8, 12, 19, 19, 19, 13] 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: 113 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361244042 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361244042 Building ZINC001361272991 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361272991 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/306 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2N(Cc2ccccc2)C1=O) `ZINC001361272991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361272991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001361272991 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2N(Cc2ccccc2)C1=O NO_LONG_NAME dock atom types: ['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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [18, 18, 18, 18, 14, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 49, 50, 50, 49, 50, 50, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 18, 18, 18, 18, 49, 49, 50, 50, 49, 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]) total number of confs: 185 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/307 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/307' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2N(Cc2ccccc2)C1=O) `ZINC001361272991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361272991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001361272991 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2N(Cc2ccccc2)C1=O NO_LONG_NAME dock atom types: ['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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [16, 16, 16, 16, 12, 1, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 48, 50, 50, 48, 50, 50, 16, 16, 16, 16, 16, 16, 16, 3, 3, 3, 3, 16, 16, 16, 16, 48, 48, 50, 50, 48, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] 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]) total number of confs: 190 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361272991 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991 Building ZINC001361272991 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361272991 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 306) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2N(Cc2ccccc2)C1=O) `ZINC001361272991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361272991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001361272991 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2N(Cc2ccccc2)C1=O NO_LONG_NAME dock atom types: ['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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [18, 18, 18, 18, 14, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 49, 50, 50, 49, 50, 50, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 18, 18, 18, 18, 49, 49, 50, 50, 49, 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]) total number of confs: 185 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 307) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2N(Cc2ccccc2)C1=O) `ZINC001361272991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361272991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001361272991 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2N(Cc2ccccc2)C1=O NO_LONG_NAME dock atom types: ['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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [16, 16, 16, 16, 12, 1, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 48, 50, 50, 48, 50, 50, 16, 16, 16, 16, 16, 16, 16, 3, 3, 3, 3, 16, 16, 16, 16, 48, 48, 50, 50, 48, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] 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]) total number of confs: 190 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361272991 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272991 Building ZINC001361272994 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361272994 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/308 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2N(Cc2ccccc2)C1=O) `ZINC001361272994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361272994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001361272994 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2N(Cc2ccccc2)C1=O NO_LONG_NAME dock atom types: ['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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [17, 17, 17, 17, 12, 1, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 49, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 17, 17, 17, 17, 49, 49, 50, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] 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]) total number of confs: 181 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/309 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2N(Cc2ccccc2)C1=O) `ZINC001361272994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361272994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001361272994 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2N(Cc2ccccc2)C1=O NO_LONG_NAME dock atom types: ['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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [18, 18, 18, 18, 14, 1, 14, 1, 1, 1, 2, 2, 1, 1, 2, 2, 18, 18, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 2, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] 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]) total number of confs: 182 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361272994 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994 Building ZINC001361272994 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361272994 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 308) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2N(Cc2ccccc2)C1=O) `ZINC001361272994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361272994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001361272994 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2N(Cc2ccccc2)C1=O NO_LONG_NAME dock atom types: ['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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [17, 17, 17, 17, 12, 1, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 49, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 17, 17, 17, 17, 49, 49, 50, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] 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]) total number of confs: 181 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 309) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2N(Cc2ccccc2)C1=O) `ZINC001361272994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361272994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001361272994 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc2N(Cc2ccccc2)C1=O NO_LONG_NAME dock atom types: ['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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.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, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [18, 18, 18, 18, 14, 1, 14, 1, 1, 1, 2, 2, 1, 1, 2, 2, 18, 18, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 2, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] 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]) total number of confs: 182 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001361272994 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001361272994 Building ZINC001545783235 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001545783235 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/310 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc(Cl)cc(Cl)c1OC(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001545783235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001545783235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001545783235 none O=C(NCc1cc(Cl)cc(Cl)c1OC(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 16, 1, 1, 16, 1, 12, 5, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 3, 7, 7, 7, 8, 10, 11, 7, 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: [3, 1, 3, 3, 16, 25, 25, 25, 25, 25, 25, 25, 25, 25, 33, 33, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 25, 25, 33, 4, 4, 4, 4] 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/311 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/311' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc(Cl)cc(Cl)c1OC(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001545783235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001545783235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001545783235 none O=C(NCc1cc(Cl)cc(Cl)c1OC(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 16, 1, 1, 16, 1, 12, 5, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 3, 7, 7, 7, 8, 10, 11, 7, 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: [3, 1, 3, 3, 15, 24, 24, 24, 24, 24, 24, 24, 24, 24, 33, 33, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 24, 24, 33, 4, 4, 4, 4] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001545783235 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235 Building ZINC001545783235 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001545783235 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 310) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1cc(Cl)cc(Cl)c1OC(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001545783235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001545783235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001545783235 none O=C(NCc1cc(Cl)cc(Cl)c1OC(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 16, 1, 1, 16, 1, 12, 5, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 3, 7, 7, 7, 8, 10, 11, 7, 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: [3, 1, 3, 3, 16, 25, 25, 25, 25, 25, 25, 25, 25, 25, 33, 33, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 25, 25, 33, 4, 4, 4, 4] 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 311) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1cc(Cl)cc(Cl)c1OC(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001545783235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001545783235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001545783235 none O=C(NCc1cc(Cl)cc(Cl)c1OC(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 16, 1, 1, 16, 1, 12, 5, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 3, 7, 7, 7, 8, 10, 11, 7, 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: [3, 1, 3, 3, 15, 24, 24, 24, 24, 24, 24, 24, 24, 24, 33, 33, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 24, 24, 33, 4, 4, 4, 4] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001545783235 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545783235 Building ZINC001545838310 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001545838310 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/312 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)C(=O)OC(C)(C)C) `ZINC001545838310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001545838310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001545838310 none CN(CCC1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 11, 12, 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, 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, 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] 0 hydrogens 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, 13, 11, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 4, 36, 46, 46, 50, 50, 50, 50, 36, 36, 36, 13, 13, 11, 11, 4, 4, 4, 4, 4, 2, 1, 2, 4, 4, 4, 4, 50, 50, 50, 50, 50, 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, 52, 53, 54, 55, 56]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/313 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/313' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)C(=O)OC(C)(C)C) `ZINC001545838310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001545838310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001545838310 none CN(CCC1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 11, 12, 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, 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, 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] 0 hydrogens 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, 18, 12, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 38, 50, 50, 50, 50, 50, 50, 38, 38, 38, 18, 18, 12, 12, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 8, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001545838310 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310 Building ZINC001545838310 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001545838310 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 312) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(CCC1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)C(=O)OC(C)(C)C) `ZINC001545838310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001545838310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001545838310 none CN(CCC1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 11, 12, 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, 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, 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] 0 hydrogens 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, 13, 11, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 4, 36, 46, 46, 50, 50, 50, 50, 36, 36, 36, 13, 13, 11, 11, 4, 4, 4, 4, 4, 2, 1, 2, 4, 4, 4, 4, 50, 50, 50, 50, 50, 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, 52, 53, 54, 55, 56]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 313) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(CCC1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)C(=O)OC(C)(C)C) `ZINC001545838310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001545838310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001545838310 none CN(CCC1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 11, 12, 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, 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, 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] 0 hydrogens 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, 18, 12, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 38, 50, 50, 50, 50, 50, 50, 38, 38, 38, 18, 18, 12, 12, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 8, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001545838310 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001545838310 Building ZINC001434872152 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001434872152 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/314 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)ccc1Oc1ccc(F)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001434872152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001434872152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001434872152 none COc1cc(C)ccc1Oc1ccc(F)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 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, 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, 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: [27, 25, 25, 25, 24, 25, 25, 25, 19, 6, 6, 6, 4, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 25, 25, 25, 25, 25, 25, 6, 4, 6, 2, 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/315 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/315' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)ccc1Oc1ccc(F)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001434872152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001434872152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001434872152 none COc1cc(C)ccc1Oc1ccc(F)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 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, 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, 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: [28, 25, 25, 25, 24, 25, 25, 25, 19, 6, 6, 6, 4, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 25, 25, 25, 25, 25, 25, 6, 2, 6, 2, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001434872152 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152 Building ZINC001434872152 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001434872152 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 314) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1cc(C)ccc1Oc1ccc(F)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001434872152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001434872152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001434872152 none COc1cc(C)ccc1Oc1ccc(F)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 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, 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, 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: [27, 25, 25, 25, 24, 25, 25, 25, 19, 6, 6, 6, 4, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 25, 25, 25, 25, 25, 25, 6, 4, 6, 2, 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 315) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1cc(C)ccc1Oc1ccc(F)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001434872152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001434872152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001434872152 none COc1cc(C)ccc1Oc1ccc(F)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 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, 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, 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: [28, 25, 25, 25, 24, 25, 25, 25, 19, 6, 6, 6, 4, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 25, 25, 25, 25, 25, 25, 6, 2, 6, 2, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001434872152 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434872152 Building ZINC001434883350 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001434883350 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/316 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1Cl) `ZINC001434883350.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001434883350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 31 natoms 30 natoms 29 natoms 28 names: ZINC001434883350 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 9, 26, 26, 25, 26, 26, 26, 26, 9, 9, 9, 8, 8, 26, 26, 26] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/317 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1Cl) `ZINC001434883350.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001434883350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 31 natoms 30 natoms 29 natoms 28 names: ZINC001434883350 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 10, 27, 27, 19, 27, 27, 27, 27, 10, 10, 10, 8, 8, 27, 27, 27] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001434883350 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350 Building ZINC001434883350 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001434883350 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 316) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1Cl) `ZINC001434883350.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001434883350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 31 natoms 30 natoms 29 natoms 28 names: ZINC001434883350 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 9, 26, 26, 25, 26, 26, 26, 26, 9, 9, 9, 8, 8, 26, 26, 26] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 317) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1Cl) `ZINC001434883350.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001434883350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 31 natoms 30 natoms 29 natoms 28 names: ZINC001434883350 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 10, 27, 27, 19, 27, 27, 27, 27, 10, 10, 10, 8, 8, 27, 27, 27] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001434883350 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434883350 Building ZINC001434887085 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001434887085 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/318 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(Oc2ccccc2)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001434887085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001434887085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001434887085 none COC(=O)c1cc(Oc2ccccc2)ccc1NC(=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', 'O.3', 'C.ar', 'C.ar', '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.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', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 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] 0 hydrogens 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, 5, 6, 5, 5, 5, 5, 22, 24, 24, 22, 24, 24, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 6, 4, 4, 4, 6, 6, 6, 5, 24, 24, 22, 24, 24, 5, 5, 2, 4, 4, 6, 6, 6, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/319 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/319' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(Oc2ccccc2)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001434887085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001434887085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001434887085 none COC(=O)c1cc(Oc2ccccc2)ccc1NC(=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', 'O.3', 'C.ar', 'C.ar', '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.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', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 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] 0 hydrogens 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, 5, 6, 5, 5, 5, 5, 22, 24, 24, 24, 24, 24, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 6, 4, 4, 4, 6, 6, 6, 5, 24, 24, 24, 24, 24, 5, 5, 2, 4, 4, 6, 6, 6, 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001434887085 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085 Building ZINC001434887085 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001434887085 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 318) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COC(=O)c1cc(Oc2ccccc2)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001434887085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001434887085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001434887085 none COC(=O)c1cc(Oc2ccccc2)ccc1NC(=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', 'O.3', 'C.ar', 'C.ar', '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.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', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 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] 0 hydrogens 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, 5, 6, 5, 5, 5, 5, 22, 24, 24, 22, 24, 24, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 6, 4, 4, 4, 6, 6, 6, 5, 24, 24, 22, 24, 24, 5, 5, 2, 4, 4, 6, 6, 6, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 319) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COC(=O)c1cc(Oc2ccccc2)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001434887085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001434887085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001434887085 none COC(=O)c1cc(Oc2ccccc2)ccc1NC(=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', 'O.3', 'C.ar', 'C.ar', '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.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', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 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] 0 hydrogens 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, 5, 6, 5, 5, 5, 5, 22, 24, 24, 24, 24, 24, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 6, 4, 4, 4, 6, 6, 6, 5, 24, 24, 24, 24, 24, 5, 5, 2, 4, 4, 6, 6, 6, 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001434887085 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434887085 Building ZINC001434911810 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434911810' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434911810 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001434911810 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434911810/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434911810 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/320 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1)C1CCCCC1) `ZINC001434911810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001434911810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434911810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001434911810 none O=C(Nc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1)C1CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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.2', 'C.2', 'Br', 'S.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 18, 50, 50, 50, 50, 50, 12, 10, 10, 10, 6, 6, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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/182395/xbh-8058088.34/working/building/ZINC001434911810 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434911810/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434911810 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/321 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/321' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1)C1CCCCC1) `ZINC001434911810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001434911810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434911810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001434911810 none O=C(Nc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1)C1CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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.2', 'C.2', 'Br', 'S.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 20, 50, 50, 50, 50, 50, 13, 10, 10, 10, 6, 6, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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/182395/xbh-8058088.34/working/building/ZINC001434911810 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001434911810 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434911810/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434911810/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434911810 Building ZINC001434911810 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434911810' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434911810 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001434911810 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434911810/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434911810 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 320) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1)C1CCCCC1) `ZINC001434911810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001434911810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434911810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001434911810 none O=C(Nc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1)C1CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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.2', 'C.2', 'Br', 'S.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 18, 50, 50, 50, 50, 50, 12, 10, 10, 10, 6, 6, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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/182395/xbh-8058088.34/working/building/ZINC001434911810 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434911810/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434911810 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 321) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1)C1CCCCC1) `ZINC001434911810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001434911810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434911810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001434911810 none O=C(Nc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1)C1CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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.2', 'C.2', 'Br', 'S.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 20, 50, 50, 50, 50, 50, 13, 10, 10, 10, 6, 6, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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/182395/xbh-8058088.34/working/building/ZINC001434911810 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001434911810 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434911810/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434911810/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434911810 Building ZINC001434912231 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001434912231 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/322 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](Cc2ccccc2C)NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC) `ZINC001434912231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001434912231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001434912231 none COc1ccc([C@@H](Cc2ccccc2C)NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 12, 5, 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, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 3, 6, 6, 10, 14, 14, 10, 14, 14, 14, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 16, 16, 16, 30, 28, 28, 28, 16, 16, 10, 10, 14, 14, 10, 14, 14, 14, 14, 3, 2, 2, 2, 2, 2, 2, 16, 30, 30, 30] 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: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/323 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/323' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](Cc2ccccc2C)NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC) `ZINC001434912231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001434912231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001434912231 none COc1ccc([C@@H](Cc2ccccc2C)NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 12, 5, 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, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 5, 3, 5, 5, 10, 14, 14, 14, 14, 14, 14, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 26, 23, 23, 23, 12, 12, 10, 10, 14, 14, 14, 14, 14, 14, 14, 3, 2, 2, 2, 2, 2, 2, 12, 26, 26, 26] 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: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001434912231 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231 Building ZINC001434912231 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001434912231 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 322) grep: /scratch/xiaobo/182395/xbh-8058088.34/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@@H](Cc2ccccc2C)NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC) `ZINC001434912231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001434912231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001434912231 none COc1ccc([C@@H](Cc2ccccc2C)NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 12, 5, 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, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 3, 6, 6, 10, 14, 14, 10, 14, 14, 14, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 16, 16, 16, 30, 28, 28, 28, 16, 16, 10, 10, 14, 14, 10, 14, 14, 14, 14, 3, 2, 2, 2, 2, 2, 2, 16, 30, 30, 30] 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: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 323) grep: /scratch/xiaobo/182395/xbh-8058088.34/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@@H](Cc2ccccc2C)NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC) `ZINC001434912231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001434912231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001434912231 none COc1ccc([C@@H](Cc2ccccc2C)NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 12, 5, 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, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 5, 3, 5, 5, 10, 14, 14, 14, 14, 14, 14, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 26, 23, 23, 23, 12, 12, 10, 10, 14, 14, 14, 14, 14, 14, 14, 3, 2, 2, 2, 2, 2, 2, 12, 26, 26, 26] 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: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001434912231 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912231 Building ZINC001434912238 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001434912238 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/324 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](Cc2ccccc2C)NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC) `ZINC001434912238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001434912238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001434912238 none COc1ccc([C@H](Cc2ccccc2C)NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 12, 5, 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, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 5, 3, 5, 5, 10, 14, 14, 10, 14, 14, 14, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 27, 25, 25, 25, 12, 12, 10, 10, 14, 14, 10, 14, 14, 14, 14, 3, 2, 2, 2, 2, 2, 2, 12, 27, 27, 27] 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/325 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/325' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](Cc2ccccc2C)NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC) `ZINC001434912238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001434912238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001434912238 none COc1ccc([C@H](Cc2ccccc2C)NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 12, 5, 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, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 6, 3, 6, 6, 10, 14, 14, 14, 14, 14, 14, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 17, 17, 17, 30, 29, 29, 29, 17, 17, 10, 10, 14, 14, 14, 14, 14, 14, 14, 3, 2, 2, 2, 2, 2, 2, 17, 30, 30, 30] 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: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001434912238 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238 Building ZINC001434912238 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001434912238 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 324) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@H](Cc2ccccc2C)NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC) `ZINC001434912238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001434912238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001434912238 none COc1ccc([C@H](Cc2ccccc2C)NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 12, 5, 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, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 5, 3, 5, 5, 10, 14, 14, 10, 14, 14, 14, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 27, 25, 25, 25, 12, 12, 10, 10, 14, 14, 10, 14, 14, 14, 14, 3, 2, 2, 2, 2, 2, 2, 12, 27, 27, 27] 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 325) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@H](Cc2ccccc2C)NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC) `ZINC001434912238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001434912238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001434912238 none COc1ccc([C@H](Cc2ccccc2C)NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 12, 5, 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, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 6, 3, 6, 6, 10, 14, 14, 14, 14, 14, 14, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 17, 17, 17, 30, 29, 29, 29, 17, 17, 10, 10, 14, 14, 14, 14, 14, 14, 14, 3, 2, 2, 2, 2, 2, 2, 17, 30, 30, 30] 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: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001434912238 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434912238 Building ZINC001434924684 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001434924684 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/326 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccc(Cl)cc3Cl)c(C)c2)cn1) `ZINC001434924684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001434924684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001434924684 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccc(Cl)cc3Cl)c(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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 5, 1, 1, 8, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 25, 25, 17, 25, 29, 29, 29, 29, 29, 29, 29, 29, 25, 25, 25, 2, 2, 3, 3, 3, 3, 3, 2, 2, 10, 10, 25, 25, 29, 29, 29, 25, 25, 25, 25, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/327 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/327' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccc(Cl)cc3Cl)c(C)c2)cn1) `ZINC001434924684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001434924684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001434924684 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccc(Cl)cc3Cl)c(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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 5, 1, 1, 8, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 25, 25, 10, 17, 30, 30, 30, 30, 30, 30, 30, 30, 25, 25, 25, 2, 2, 4, 4, 4, 4, 4, 2, 2, 10, 10, 25, 25, 30, 30, 30, 25, 25, 25, 25, 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001434924684 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684 Building ZINC001434924684 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001434924684 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 326) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccc(Cl)cc3Cl)c(C)c2)cn1) `ZINC001434924684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001434924684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001434924684 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccc(Cl)cc3Cl)c(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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 5, 1, 1, 8, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 25, 25, 17, 25, 29, 29, 29, 29, 29, 29, 29, 29, 25, 25, 25, 2, 2, 3, 3, 3, 3, 3, 2, 2, 10, 10, 25, 25, 29, 29, 29, 25, 25, 25, 25, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 327) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccc(Cl)cc3Cl)c(C)c2)cn1) `ZINC001434924684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001434924684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001434924684 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccc(Cl)cc3Cl)c(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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 5, 1, 1, 8, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 25, 25, 10, 17, 30, 30, 30, 30, 30, 30, 30, 30, 25, 25, 25, 2, 2, 4, 4, 4, 4, 4, 2, 2, 10, 10, 25, 25, 30, 30, 30, 25, 25, 25, 25, 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001434924684 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434924684 Building ZINC001434942917 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001434942917 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/328 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(Sc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c(C)c2)n1) `ZINC001434942917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001434942917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001434942917 none Cc1csc(Sc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c(C)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'S.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.3', 'C.ar', '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, 1, 1, 14, 1, 14, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 50, 50, 50, 50, 50, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/329 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/329' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(Sc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c(C)c2)n1) `ZINC001434942917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001434942917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001434942917 none Cc1csc(Sc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c(C)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'S.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.3', 'C.ar', '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, 1, 1, 14, 1, 14, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 50, 50, 50, 50, 50, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001434942917 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917 Building ZINC001434942917 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001434942917 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 328) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1csc(Sc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c(C)c2)n1) `ZINC001434942917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001434942917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001434942917 none Cc1csc(Sc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c(C)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'S.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.3', 'C.ar', '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, 1, 1, 14, 1, 14, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 50, 50, 50, 50, 50, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 329) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1csc(Sc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c(C)c2)n1) `ZINC001434942917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001434942917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001434942917 none Cc1csc(Sc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c(C)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'S.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.3', 'C.ar', '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, 1, 1, 14, 1, 14, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 50, 50, 50, 50, 50, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001434942917 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001434942917 Building ZINC001435002543 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435002543 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/330 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCOc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1OC) `ZINC001435002543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435002543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001435002543 none CCN(CC)CCOc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens 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, 25, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 6, 6, 6, 6, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 6, 2, 2, 1, 2, 6, 6, 11, 11, 11] 50 rigid atoms, others: [12, 15, 16, 14] 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]) total number of confs: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/331 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/331' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCOc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1OC) `ZINC001435002543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435002543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001435002543 none CCN(CC)CCOc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens 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, 26, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 6, 6, 6, 6, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 46, 46, 6, 2, 2, 1, 2, 6, 6, 12, 12, 12] 50 rigid atoms, others: [12, 15, 16, 14] 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]) total number of confs: 166 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435002543 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543 Building ZINC001435002543 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435002543 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 330) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCN(CC)CCOc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1OC) `ZINC001435002543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435002543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001435002543 none CCN(CC)CCOc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens 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, 25, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 6, 6, 6, 6, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 6, 2, 2, 1, 2, 6, 6, 11, 11, 11] 50 rigid atoms, others: [12, 15, 16, 14] 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]) total number of confs: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 331) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCN(CC)CCOc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1OC) `ZINC001435002543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435002543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001435002543 none CCN(CC)CCOc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens 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, 26, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 6, 6, 6, 6, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 46, 46, 6, 2, 2, 1, 2, 6, 6, 12, 12, 12] 50 rigid atoms, others: [12, 15, 16, 14] 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]) total number of confs: 166 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435002543 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435002543 Building ZINC001435014396 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435014396 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/332 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(COc2ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)c1) `ZINC001435014396.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435014396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435014396 none Cc1cccc(COc2ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 44, 13, 44, 44, 7, 7, 6, 6, 7, 7, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 44, 44, 44, 44, 13, 44, 44, 7, 7, 7, 7, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 7, 7, 44] 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, 57]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/333 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/333' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(COc2ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)c1) `ZINC001435014396.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435014396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435014396 none Cc1cccc(COc2ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 14, 40, 40, 8, 8, 6, 4, 8, 8, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 40, 40, 40, 40, 14, 40, 40, 8, 8, 8, 8, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 8, 8, 40] 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, 57]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435014396 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396 Building ZINC001435014396 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435014396 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 332) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc(COc2ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)c1) `ZINC001435014396.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435014396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435014396 none Cc1cccc(COc2ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 44, 13, 44, 44, 7, 7, 6, 6, 7, 7, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 44, 44, 44, 44, 13, 44, 44, 7, 7, 7, 7, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 7, 7, 44] 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, 57]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 333) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc(COc2ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)c1) `ZINC001435014396.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435014396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435014396 none Cc1cccc(COc2ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 14, 40, 40, 8, 8, 6, 4, 8, 8, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 40, 40, 40, 40, 14, 40, 40, 8, 8, 8, 8, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 8, 8, 40] 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, 57]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435014396 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014396 Building ZINC001435014397 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435014397 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/334 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(COc2ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)c1) `ZINC001435014397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435014397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435014397 none Cc1cccc(COc2ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 13, 40, 40, 8, 8, 4, 4, 8, 8, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 40, 40, 40, 40, 16, 40, 40, 8, 8, 8, 8, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 8, 8, 40] 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, 57]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/335 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/335' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(COc2ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)c1) `ZINC001435014397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435014397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435014397 none Cc1cccc(COc2ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 44, 8, 44, 44, 7, 7, 4, 4, 7, 7, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 44, 44, 44, 44, 13, 44, 44, 7, 7, 7, 7, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 7, 7, 44] 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, 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/182395/xbh-8058088.34/working/building/ZINC001435014397 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435014397 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397 Building ZINC001435014397 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435014397 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 334) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc(COc2ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)c1) `ZINC001435014397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435014397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435014397 none Cc1cccc(COc2ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 13, 40, 40, 8, 8, 4, 4, 8, 8, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 40, 40, 40, 40, 16, 40, 40, 8, 8, 8, 8, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 8, 8, 40] 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, 57]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 335) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc(COc2ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)c1) `ZINC001435014397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435014397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435014397 none Cc1cccc(COc2ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 44, 8, 44, 44, 7, 7, 4, 4, 7, 7, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 44, 44, 44, 44, 13, 44, 44, 7, 7, 7, 7, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 7, 7, 44] 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, 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/182395/xbh-8058088.34/working/building/ZINC001435014397 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435014397 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435014397 Building ZINC001435017888 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435017888 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/336 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@@H](C)O1) `ZINC001435017888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435017888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435017888 none C[C@@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', '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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 5, 12, 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, 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] 0 hydrogens 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, 23, 5, 17, 17, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 17, 4, 9, 9, 17, 28, 28, 28, 28, 28] 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/337 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/337' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@@H](C)O1) `ZINC001435017888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435017888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435017888 none C[C@@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', '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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 5, 12, 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, 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] 0 hydrogens 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, 20, 5, 17, 17, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 17, 4, 9, 9, 17, 28, 28, 28, 28, 28] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435017888 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888 Building ZINC001435017888 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435017888 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 336) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@@H](C)O1) `ZINC001435017888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435017888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435017888 none C[C@@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', '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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 5, 12, 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, 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] 0 hydrogens 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, 23, 5, 17, 17, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 17, 4, 9, 9, 17, 28, 28, 28, 28, 28] 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 337) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@@H](C)O1) `ZINC001435017888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435017888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435017888 none C[C@@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', '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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 5, 12, 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, 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] 0 hydrogens 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, 20, 5, 17, 17, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 17, 4, 9, 9, 17, 28, 28, 28, 28, 28] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435017888 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017888 Building ZINC001435017914 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435017914 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/338 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@H](C)O1) `ZINC001435017914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435017914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435017914 none C[C@@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', '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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 5, 12, 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, 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] 0 hydrogens 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, 30, 29, 18, 5, 15, 15, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 29, 31, 29, 32, 32, 32, 32, 32, 29, 29, 15, 15, 4, 9, 9, 15, 29, 29, 32, 32, 32] 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/339 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/339' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@H](C)O1) `ZINC001435017914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435017914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435017914 none C[C@@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', '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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 5, 12, 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, 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] 0 hydrogens 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, 5, 3, 16, 16, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 16, 16, 3, 9, 9, 16, 29, 29, 29, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435017914 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914 Building ZINC001435017914 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435017914 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 338) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@H](C)O1) `ZINC001435017914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435017914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435017914 none C[C@@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', '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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 5, 12, 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, 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] 0 hydrogens 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, 30, 29, 18, 5, 15, 15, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 29, 31, 29, 32, 32, 32, 32, 32, 29, 29, 15, 15, 4, 9, 9, 15, 29, 29, 32, 32, 32] 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 339) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@H](C)O1) `ZINC001435017914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435017914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435017914 none C[C@@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', '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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 5, 12, 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, 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] 0 hydrogens 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, 5, 3, 16, 16, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 16, 16, 3, 9, 9, 16, 29, 29, 29, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435017914 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017914 Building ZINC001435017918 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435017918 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/340 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@H](C)O1) `ZINC001435017918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435017918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435017918 none C[C@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', '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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 5, 12, 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, 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] 0 hydrogens 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, 10, 5, 17, 17, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 17, 4, 8, 8, 17, 28, 28, 28, 28, 28] 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/341 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/341' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@H](C)O1) `ZINC001435017918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435017918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435017918 none C[C@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', '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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 5, 12, 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, 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] 0 hydrogens 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, 12, 4, 17, 17, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 17, 4, 9, 9, 17, 28, 28, 28, 28, 28] 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435017918 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918 Building ZINC001435017918 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435017918 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 340) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@H](C)O1) `ZINC001435017918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435017918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435017918 none C[C@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', '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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 5, 12, 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, 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] 0 hydrogens 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, 10, 5, 17, 17, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 17, 4, 8, 8, 17, 28, 28, 28, 28, 28] 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 341) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@H](C)O1) `ZINC001435017918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435017918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435017918 none C[C@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', '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', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 5, 12, 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, 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] 0 hydrogens 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, 12, 4, 17, 17, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 17, 4, 9, 9, 17, 28, 28, 28, 28, 28] 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435017918 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435017918 Building ZINC001435027569 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435027569 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/342 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n(c2ccc(C(F)(F)F)cn2)n1) `ZINC001435027569.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435027569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001435027569 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n(c2ccc(C(F)(F)F)cn2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'N.2', '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, 1, 16, 1, 1, 16, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 6, 1, 6, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 27, 27, 39, 39, 39, 39, 39, 39, 39, 39, 39, 27, 27, 27, 27, 27, 16, 5, 1, 5, 39, 39, 39] 50 rigid atoms, others: [5, 7, 8, 9] 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/343 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/343' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n(c2ccc(C(F)(F)F)cn2)n1) `ZINC001435027569.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435027569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001435027569 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n(c2ccc(C(F)(F)F)cn2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'N.2', '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, 1, 16, 1, 1, 16, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 6, 1, 6, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 27, 27, 39, 39, 39, 39, 39, 39, 39, 39, 39, 27, 27, 27, 27, 27, 16, 5, 1, 5, 39, 39, 39] 50 rigid atoms, others: [5, 7, 8, 9] 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435027569 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569 Building ZINC001435027569 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435027569 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 342) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n(c2ccc(C(F)(F)F)cn2)n1) `ZINC001435027569.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435027569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001435027569 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n(c2ccc(C(F)(F)F)cn2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'N.2', '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, 1, 16, 1, 1, 16, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 6, 1, 6, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 27, 27, 39, 39, 39, 39, 39, 39, 39, 39, 39, 27, 27, 27, 27, 27, 16, 5, 1, 5, 39, 39, 39] 50 rigid atoms, others: [5, 7, 8, 9] 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 343) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n(c2ccc(C(F)(F)F)cn2)n1) `ZINC001435027569.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435027569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001435027569 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n(c2ccc(C(F)(F)F)cn2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'N.2', '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, 1, 16, 1, 1, 16, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 6, 1, 6, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 27, 27, 39, 39, 39, 39, 39, 39, 39, 39, 39, 27, 27, 27, 27, 27, 16, 5, 1, 5, 39, 39, 39] 50 rigid atoms, others: [5, 7, 8, 9] 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435027569 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435027569 Building ZINC001435043748 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435043748 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/344 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(C(F)(F)F)c(c2ccc(Cl)cc2)c1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001435043748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435043748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001435043748 none Cn1nc(C(F)(F)F)c(c2ccc(Cl)cc2)c1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 8, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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, 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] 0 hydrogens 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, 45, 45, 45, 45, 45, 45, 48, 48, 45, 45, 48, 48, 15, 6, 1, 6, 1, 1, 1, 5, 5, 2, 2, 5, 5, 45, 45, 45, 48, 48, 48, 48, 15, 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/345 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/345' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(C(F)(F)F)c(c2ccc(Cl)cc2)c1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001435043748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435043748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001435043748 none Cn1nc(C(F)(F)F)c(c2ccc(Cl)cc2)c1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 8, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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, 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] 0 hydrogens 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, 45, 45, 45, 45, 45, 45, 48, 48, 48, 48, 48, 48, 15, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 45, 45, 45, 48, 48, 48, 48, 15, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435043748 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748 Building ZINC001435043748 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435043748 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 344) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cn1nc(C(F)(F)F)c(c2ccc(Cl)cc2)c1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001435043748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435043748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001435043748 none Cn1nc(C(F)(F)F)c(c2ccc(Cl)cc2)c1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 8, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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, 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] 0 hydrogens 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, 45, 45, 45, 45, 45, 45, 48, 48, 45, 45, 48, 48, 15, 6, 1, 6, 1, 1, 1, 5, 5, 2, 2, 5, 5, 45, 45, 45, 48, 48, 48, 48, 15, 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 345) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cn1nc(C(F)(F)F)c(c2ccc(Cl)cc2)c1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001435043748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435043748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001435043748 none Cn1nc(C(F)(F)F)c(c2ccc(Cl)cc2)c1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 8, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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, 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] 0 hydrogens 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, 45, 45, 45, 45, 45, 45, 48, 48, 48, 48, 48, 48, 15, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 45, 45, 45, 48, 48, 48, 48, 15, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435043748 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435043748 Building ZINC001435062975 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435062975 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/346 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN(Cc1ccc(C(F)(F)F)cc1)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435062975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435062975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435062975 none CN(C)CCN(Cc1ccc(C(F)(F)F)cc1)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 20, 24, 16, 7, 3, 7, 16, 22, 22, 19, 22, 22, 22, 22, 22, 22, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 24, 24, 24, 24, 24, 20, 20, 16, 16, 16, 16, 22, 22, 22, 22, 3, 1, 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]) total number of confs: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/347 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/347' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN(Cc1ccc(C(F)(F)F)cc1)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435062975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435062975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435062975 none CN(C)CCN(Cc1ccc(C(F)(F)F)cc1)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 27, 17, 8, 4, 8, 18, 25, 25, 22, 25, 25, 25, 25, 25, 25, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 27, 27, 27, 27, 27, 27, 22, 22, 17, 17, 18, 18, 25, 25, 25, 25, 3, 1, 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]) total number of confs: 188 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435062975 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975 Building ZINC001435062975 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435062975 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 346) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(C)CCN(Cc1ccc(C(F)(F)F)cc1)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435062975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435062975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435062975 none CN(C)CCN(Cc1ccc(C(F)(F)F)cc1)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 20, 24, 16, 7, 3, 7, 16, 22, 22, 19, 22, 22, 22, 22, 22, 22, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 24, 24, 24, 24, 24, 20, 20, 16, 16, 16, 16, 22, 22, 22, 22, 3, 1, 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]) total number of confs: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 347) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(C)CCN(Cc1ccc(C(F)(F)F)cc1)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435062975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435062975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435062975 none CN(C)CCN(Cc1ccc(C(F)(F)F)cc1)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 27, 17, 8, 4, 8, 18, 25, 25, 22, 25, 25, 25, 25, 25, 25, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 27, 27, 27, 27, 27, 27, 22, 22, 17, 17, 18, 18, 25, 25, 25, 25, 3, 1, 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]) total number of confs: 188 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435062975 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435062975 Building ZINC001435066018 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435066018 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/348 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCC[C@@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435066018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435066018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435066018 none C[C@@H]1CCCC[C@@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 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] 0 hydrogens 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, 9, 9, 9, 9, 9, 6, 9, 12, 21, 33, 33, 46, 46, 46, 46, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 21, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 3, 1, 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, 53, 54, 55, 56]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/349 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/349' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCC[C@@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435066018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435066018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435066018 none C[C@@H]1CCCC[C@@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 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] 0 hydrogens 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, 9, 9, 9, 9, 9, 6, 9, 12, 22, 33, 33, 45, 45, 45, 45, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 22, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 3, 1, 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, 53, 54, 55, 56]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435066018 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018 Building ZINC001435066018 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435066018 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 348) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@H]1CCCC[C@@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435066018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435066018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435066018 none C[C@@H]1CCCC[C@@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 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] 0 hydrogens 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, 9, 9, 9, 9, 9, 6, 9, 12, 21, 33, 33, 46, 46, 46, 46, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 21, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 3, 1, 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, 53, 54, 55, 56]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 349) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@H]1CCCC[C@@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435066018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435066018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435066018 none C[C@@H]1CCCC[C@@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 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] 0 hydrogens 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, 9, 9, 9, 9, 9, 6, 9, 12, 22, 33, 33, 45, 45, 45, 45, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 22, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 3, 1, 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, 53, 54, 55, 56]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435066018 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066018 Building ZINC001435066019 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435066019 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/350 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCC[C@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435066019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435066019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435066019 none C[C@@H]1CCCC[C@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 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] 0 hydrogens 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, 9, 9, 9, 9, 9, 7, 9, 15, 27, 38, 38, 46, 46, 46, 46, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 27, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 3, 1, 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, 53, 54, 55, 56]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/351 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/351' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCC[C@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435066019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435066019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435066019 none C[C@@H]1CCCC[C@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 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] 0 hydrogens 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, 9, 9, 9, 9, 9, 7, 9, 15, 27, 37, 37, 47, 47, 47, 47, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 27, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 3, 1, 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, 53, 54, 55, 56]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435066019 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019 Building ZINC001435066019 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435066019 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 350) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@H]1CCCC[C@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435066019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435066019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435066019 none C[C@@H]1CCCC[C@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 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] 0 hydrogens 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, 9, 9, 9, 9, 9, 7, 9, 15, 27, 38, 38, 46, 46, 46, 46, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 27, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 3, 1, 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, 53, 54, 55, 56]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 351) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@H]1CCCC[C@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435066019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435066019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435066019 none C[C@@H]1CCCC[C@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 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] 0 hydrogens 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, 9, 9, 9, 9, 9, 7, 9, 15, 27, 37, 37, 47, 47, 47, 47, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 27, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 3, 1, 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, 53, 54, 55, 56]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435066019 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066019 Building ZINC001435066020 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435066020 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/352 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCC[C@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435066020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435066020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435066020 none C[C@H]1CCCC[C@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 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] 0 hydrogens 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, 9, 9, 9, 9, 9, 6, 9, 13, 24, 35, 35, 44, 44, 44, 44, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 24, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 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, 53, 54, 55, 56]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/353 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/353' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCC[C@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435066020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435066020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435066020 none C[C@H]1CCCC[C@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 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] 0 hydrogens 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, 9, 9, 9, 9, 9, 6, 9, 13, 22, 34, 34, 47, 47, 47, 47, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 22, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 3, 1, 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, 53, 54, 55, 56]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435066020 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020 Building ZINC001435066020 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435066020 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 352) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@H]1CCCC[C@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435066020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435066020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435066020 none C[C@H]1CCCC[C@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 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] 0 hydrogens 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, 9, 9, 9, 9, 9, 6, 9, 13, 24, 35, 35, 44, 44, 44, 44, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 24, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 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, 53, 54, 55, 56]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 353) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@H]1CCCC[C@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435066020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435066020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435066020 none C[C@H]1CCCC[C@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 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] 0 hydrogens 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, 9, 9, 9, 9, 9, 6, 9, 13, 22, 34, 34, 47, 47, 47, 47, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 22, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 3, 1, 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, 53, 54, 55, 56]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435066020 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066020 Building ZINC001435066021 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435066021 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/354 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCC[C@@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435066021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435066021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435066021 none C[C@H]1CCCC[C@@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 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] 0 hydrogens 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, 9, 9, 9, 9, 9, 6, 9, 15, 25, 36, 36, 47, 47, 47, 47, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 3, 1, 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, 53, 54, 55, 56]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/355 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/355' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCC[C@@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435066021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435066021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435066021 none C[C@H]1CCCC[C@@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 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] 0 hydrogens 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, 8, 8, 8, 8, 4, 8, 14, 24, 35, 35, 46, 46, 46, 46, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 24, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 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, 53, 54, 55, 56]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435066021 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021 Building ZINC001435066021 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435066021 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 354) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@H]1CCCC[C@@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435066021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435066021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435066021 none C[C@H]1CCCC[C@@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 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] 0 hydrogens 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, 9, 9, 9, 9, 9, 6, 9, 15, 25, 36, 36, 47, 47, 47, 47, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 3, 1, 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, 53, 54, 55, 56]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 355) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@H]1CCCC[C@@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435066021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435066021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435066021 none C[C@H]1CCCC[C@@]1(CNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 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] 0 hydrogens 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, 8, 8, 8, 8, 4, 8, 14, 24, 35, 35, 46, 46, 46, 46, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 24, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 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, 53, 54, 55, 56]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435066021 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435066021 Building ZINC001435074455 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435074455 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/356 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2ccc3nc(C)[nH]c3c2)cc1) `ZINC001435074455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435074455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001435074455 none COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2ccc3nc(C)[nH]c3c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 8, 6, 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, 3, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 21, 26, 26, 20, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 20, 20, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25, 26, 26] 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/357 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/357' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2ccc3nc(C)[nH]c3c2)cc1) `ZINC001435074455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435074455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001435074455 none COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2ccc3nc(C)[nH]c3c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 8, 6, 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, 3, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 7, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 29, 29, 29, 29, 29, 29, 29, 22, 22, 3, 3, 3, 3, 3, 3, 26, 26, 26, 26, 26, 26, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435074455 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455 Building ZINC001435074455 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435074455 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 356) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2ccc3nc(C)[nH]c3c2)cc1) `ZINC001435074455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435074455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001435074455 none COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2ccc3nc(C)[nH]c3c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 8, 6, 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, 3, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 21, 26, 26, 20, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 20, 20, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25, 26, 26] 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 357) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2ccc3nc(C)[nH]c3c2)cc1) `ZINC001435074455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435074455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001435074455 none COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2ccc3nc(C)[nH]c3c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 8, 6, 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, 3, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 7, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 29, 29, 29, 29, 29, 29, 29, 22, 22, 3, 3, 3, 3, 3, 3, 26, 26, 26, 26, 26, 26, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435074455 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435074455 Building ZINC001435081184 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435081184 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/358 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(Br)cc1CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CC1) `ZINC001435081184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435081184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001435081184 none CCOc1ccc(Br)cc1CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'C.3', '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, 17, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 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, 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] 0 hydrogens 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, 19, 19, 19, 18, 19, 19, 19, 14, 7, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 8, 8, 32, 32, 32, 32, 32, 19, 19, 19, 14, 14, 7, 7, 8, 8, 8, 8, 8] 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]) total number of confs: 104 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/359 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/359' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(Br)cc1CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CC1) `ZINC001435081184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435081184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001435081184 none CCOc1ccc(Br)cc1CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'C.3', '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, 17, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 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, 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] 0 hydrogens 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, 33, 20, 20, 20, 20, 20, 20, 20, 17, 8, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 8, 9, 9, 35, 35, 35, 35, 35, 20, 20, 20, 17, 17, 5, 5, 9, 9, 9, 9, 9] 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]) total number of confs: 125 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435081184 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184 Building ZINC001435081184 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435081184 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 358) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCOc1ccc(Br)cc1CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CC1) `ZINC001435081184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435081184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001435081184 none CCOc1ccc(Br)cc1CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'C.3', '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, 17, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 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, 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] 0 hydrogens 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, 19, 19, 19, 18, 19, 19, 19, 14, 7, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 8, 8, 32, 32, 32, 32, 32, 19, 19, 19, 14, 14, 7, 7, 8, 8, 8, 8, 8] 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]) total number of confs: 104 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 359) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCOc1ccc(Br)cc1CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CC1) `ZINC001435081184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435081184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001435081184 none CCOc1ccc(Br)cc1CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'C.3', '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, 17, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 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, 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] 0 hydrogens 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, 33, 20, 20, 20, 20, 20, 20, 20, 17, 8, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 8, 9, 9, 35, 35, 35, 35, 35, 20, 20, 20, 17, 17, 5, 5, 9, 9, 9, 9, 9] 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]) total number of confs: 125 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435081184 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435081184 Building ZINC001435126350 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435126350 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/360 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Br)cc1Oc1ccccc1) `ZINC001435126350.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435126350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001435126350 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Br)cc1Oc1ccccc1 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', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations 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, 2, 2, 2, 14, 36, 36, 24, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 36, 36, 36, 50, 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/361 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/361' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(Br)cc1Oc1ccccc1) `ZINC001435126350.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435126350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001435126350 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(Br)cc1Oc1ccccc1 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', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations 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, 2, 2, 2, 14, 35, 35, 25, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 35, 35, 35, 50, 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435126350 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350 Building ZINC001435126350 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435126350 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 360) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Br)cc1Oc1ccccc1) `ZINC001435126350.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435126350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001435126350 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Br)cc1Oc1ccccc1 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', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations 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, 2, 2, 2, 14, 36, 36, 24, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 36, 36, 36, 50, 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 361) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(Br)cc1Oc1ccccc1) `ZINC001435126350.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435126350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001435126350 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(Br)cc1Oc1ccccc1 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', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations 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, 2, 2, 2, 14, 35, 35, 25, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 35, 35, 35, 50, 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435126350 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435126350 Building ZINC001435144254 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435144254 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/362 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N(c2ccccc2F)C2CCN(C(=O)OC(C)(C)C)CC2)c1) `ZINC001435144254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435144254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001435144254 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N(c2ccccc2F)C2CCN(C(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 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] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 3, 8, 8, 6, 8, 8, 8, 3, 10, 10, 10, 10, 20, 20, 21, 21, 21, 21, 10, 10, 4, 4, 4, 4, 2, 4, 4, 8, 8, 6, 8, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 93 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/363 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/363' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N(c2ccccc2F)C2CCN(C(=O)OC(C)(C)C)CC2)c1) `ZINC001435144254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435144254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001435144254 none Cc1cccc([C@]([O-])([SiH3])C(=O)N(c2ccccc2F)C2CCN(C(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 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] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 3, 7, 7, 3, 7, 7, 7, 3, 12, 12, 12, 12, 21, 21, 22, 22, 22, 22, 12, 12, 4, 4, 4, 4, 2, 4, 4, 7, 7, 6, 7, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 12, 12, 12, 12, 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, 59, 60]) total number of confs: 104 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435144254 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254 Building ZINC001435144254 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435144254 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 362) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N(c2ccccc2F)C2CCN(C(=O)OC(C)(C)C)CC2)c1) `ZINC001435144254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435144254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001435144254 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N(c2ccccc2F)C2CCN(C(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 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] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 3, 8, 8, 6, 8, 8, 8, 3, 10, 10, 10, 10, 20, 20, 21, 21, 21, 21, 10, 10, 4, 4, 4, 4, 2, 4, 4, 8, 8, 6, 8, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 93 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 363) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N(c2ccccc2F)C2CCN(C(=O)OC(C)(C)C)CC2)c1) `ZINC001435144254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435144254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001435144254 none Cc1cccc([C@]([O-])([SiH3])C(=O)N(c2ccccc2F)C2CCN(C(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 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] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 3, 7, 7, 3, 7, 7, 7, 3, 12, 12, 12, 12, 21, 21, 22, 22, 22, 22, 12, 12, 4, 4, 4, 4, 2, 4, 4, 7, 7, 6, 7, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 12, 12, 12, 12, 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, 59, 60]) total number of confs: 104 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435144254 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435144254 Building ZINC001435148558 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435148558 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/364 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(c3nc4ccc(F)cc4n3C(C)C)cc2C)cn1) `ZINC001435148558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435148558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435148558 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(c3nc4ccc(F)cc4n3C(C)C)cc2C)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 6, 6, 3, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 6, 2, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 6, 6, 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, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/365 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/365' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(c3nc4ccc(F)cc4n3C(C)C)cc2C)cn1) `ZINC001435148558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435148558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435148558 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(c3nc4ccc(F)cc4n3C(C)C)cc2C)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 2, 18, 22, 22, 24, 24, 24, 23, 22, 18, 18, 20, 20, 6, 6, 6, 5, 5, 14, 14, 14, 14, 14, 5, 2, 6, 6, 23, 24, 23, 18, 19, 22, 22, 18, 22, 22, 6, 6, 6, 6, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435148558 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558 Building ZINC001435148558 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435148558 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 364) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(c3nc4ccc(F)cc4n3C(C)C)cc2C)cn1) `ZINC001435148558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435148558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435148558 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(c3nc4ccc(F)cc4n3C(C)C)cc2C)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 6, 6, 3, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 6, 2, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 6, 6, 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, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 365) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(c3nc4ccc(F)cc4n3C(C)C)cc2C)cn1) `ZINC001435148558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435148558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435148558 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(c3nc4ccc(F)cc4n3C(C)C)cc2C)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 2, 18, 22, 22, 24, 24, 24, 23, 22, 18, 18, 20, 20, 6, 6, 6, 5, 5, 14, 14, 14, 14, 14, 5, 2, 6, 6, 23, 24, 23, 18, 19, 22, 22, 18, 22, 22, 6, 6, 6, 6, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435148558 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435148558 Building ZINC001435150484 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435150484 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/366 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2c(C)cccc2c2nc3ccc(F)cc3n2C(C)C)cn1) `ZINC001435150484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435150484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435150484 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2c(C)cccc2c2nc3ccc(F)cc3n2C(C)C)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 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, 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, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 15, 15, 15, 15, 15, 7, 3, 12, 12, 12, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/367 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/367' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2c(C)cccc2c2nc3ccc(F)cc3n2C(C)C)cn1) `ZINC001435150484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435150484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435150484 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2c(C)cccc2c2nc3ccc(F)cc3n2C(C)C)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 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, 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, 7, 7, 7] 0 hydrogens 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, 7, 7, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 14, 14, 14, 14, 14, 7, 3, 12, 12, 12, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435150484 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484 Building ZINC001435150484 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435150484 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 366) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2c(C)cccc2c2nc3ccc(F)cc3n2C(C)C)cn1) `ZINC001435150484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435150484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435150484 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2c(C)cccc2c2nc3ccc(F)cc3n2C(C)C)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 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, 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, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 15, 15, 15, 15, 15, 7, 3, 12, 12, 12, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 367) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2c(C)cccc2c2nc3ccc(F)cc3n2C(C)C)cn1) `ZINC001435150484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435150484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435150484 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2c(C)cccc2c2nc3ccc(F)cc3n2C(C)C)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 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, 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, 7, 7, 7] 0 hydrogens 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, 7, 7, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 14, 14, 14, 14, 14, 7, 3, 12, 12, 12, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435150484 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435150484 Building ZINC001435154330 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435154330 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/368 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/368' -> `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)(C)c1cccc(F)c1) `ZINC001435154330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435154330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435154330 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)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', 'C.3', 'C.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', 'H', 'H', 'H'] dock atom type 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, 1, 1, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 13, 13, 13, 13, 13, 13, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 40, 41, 2, 14, 15, 16, 17, 18, 19, 4, 39] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/369 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/369' -> `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)(C)c1cccc(F)c1) `ZINC001435154330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435154330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435154330 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)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', 'C.3', 'C.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', 'H', 'H', 'H'] dock atom type 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, 1, 1, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 13, 13, 13, 13, 13, 13, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 40, 41, 2, 14, 15, 16, 17, 18, 19, 4, 39] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435154330 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330 Building ZINC001435154330 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435154330 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 368) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)c1cccc(F)c1) `ZINC001435154330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435154330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435154330 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)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', 'C.3', 'C.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', 'H', 'H', 'H'] dock atom type 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, 1, 1, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 13, 13, 13, 13, 13, 13, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 40, 41, 2, 14, 15, 16, 17, 18, 19, 4, 39] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 369) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)c1cccc(F)c1) `ZINC001435154330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435154330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435154330 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)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', 'C.3', 'C.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', 'H', 'H', 'H'] dock atom type 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, 1, 1, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 13, 13, 13, 13, 13, 13, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 40, 41, 2, 14, 15, 16, 17, 18, 19, 4, 39] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435154330 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435154330 Building ZINC001435169746 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435169746 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/370 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1Oc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001435169746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435169746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435169746 none COc1ccccc1Oc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'Br', 'S.3', '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, 12, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens 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, 48, 9, 9, 28, 28, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 28, 28, 50, 50, 50, 50, 50, 50, 50, 28, 28, 9, 9, 2, 2, 2, 28, 28] 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/371 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1Oc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001435169746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435169746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435169746 none COc1ccccc1Oc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'Br', 'S.3', '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, 12, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens 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, 28, 23, 28, 28, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 28, 28, 50, 50, 50, 50, 50, 50, 50, 28, 28, 9, 9, 2, 2, 2, 28, 28] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435169746 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746 Building ZINC001435169746 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435169746 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 370) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccccc1Oc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001435169746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435169746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435169746 none COc1ccccc1Oc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'Br', 'S.3', '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, 12, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens 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, 48, 9, 9, 28, 28, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 28, 28, 50, 50, 50, 50, 50, 50, 50, 28, 28, 9, 9, 2, 2, 2, 28, 28] 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 371) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccccc1Oc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001435169746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435169746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435169746 none COc1ccccc1Oc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'Br', 'S.3', '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, 12, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens 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, 28, 23, 28, 28, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 28, 28, 50, 50, 50, 50, 50, 50, 50, 28, 28, 9, 9, 2, 2, 2, 28, 28] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435169746 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435169746 Building ZINC001435177623 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435177623 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/372 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCC2(c3ccc(OC)c(OC)c3)CCCCC2)cc1Cl) `ZINC001435177623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435177623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435177623 none COc1ccc([C@]([O-])([SiH3])C(=O)NCC2(c3ccc(OC)c(OC)c3)CCCCC2)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', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 10, 12, 16, 16, 16, 16, 27, 16, 16, 24, 16, 12, 12, 12, 12, 12, 4, 4, 4, 7, 7, 7, 4, 4, 2, 7, 7, 16, 16, 27, 27, 27, 24, 24, 24, 16, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/373 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/373' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCC2(c3ccc(OC)c(OC)c3)CCCCC2)cc1Cl) `ZINC001435177623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435177623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435177623 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCC2(c3ccc(OC)c(OC)c3)CCCCC2)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', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 11, 15, 15, 15, 15, 26, 15, 15, 23, 15, 11, 11, 11, 11, 11, 4, 4, 4, 8, 8, 8, 4, 4, 2, 6, 6, 15, 15, 26, 26, 26, 23, 23, 23, 15, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435177623 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623 Building ZINC001435177623 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435177623 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 372) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCC2(c3ccc(OC)c(OC)c3)CCCCC2)cc1Cl) `ZINC001435177623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435177623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435177623 none COc1ccc([C@]([O-])([SiH3])C(=O)NCC2(c3ccc(OC)c(OC)c3)CCCCC2)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', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 10, 12, 16, 16, 16, 16, 27, 16, 16, 24, 16, 12, 12, 12, 12, 12, 4, 4, 4, 7, 7, 7, 4, 4, 2, 7, 7, 16, 16, 27, 27, 27, 24, 24, 24, 16, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 373) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCC2(c3ccc(OC)c(OC)c3)CCCCC2)cc1Cl) `ZINC001435177623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435177623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435177623 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCC2(c3ccc(OC)c(OC)c3)CCCCC2)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', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 11, 15, 15, 15, 15, 26, 15, 15, 23, 15, 11, 11, 11, 11, 11, 4, 4, 4, 8, 8, 8, 4, 4, 2, 6, 6, 15, 15, 26, 26, 26, 23, 23, 23, 15, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435177623 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435177623 Building ZINC001435196757 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435196757 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/374 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1cn(c2ccccc2)nc1c1ccc(F)cc1) `ZINC001435196757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435196757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435196757 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1cn(c2ccccc2)nc1c1ccc(F)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.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 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: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 20, 20, 50, 50, 50, 50, 50, 50, 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/375 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/375' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1cn(c2ccccc2)nc1c1ccc(F)cc1) `ZINC001435196757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435196757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435196757 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1cn(c2ccccc2)nc1c1ccc(F)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.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 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: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 20, 20, 50, 50, 50, 50, 50, 50, 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435196757 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757 Building ZINC001435196757 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435196757 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 374) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1cn(c2ccccc2)nc1c1ccc(F)cc1) `ZINC001435196757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435196757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435196757 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1cn(c2ccccc2)nc1c1ccc(F)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.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 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: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 20, 20, 50, 50, 50, 50, 50, 50, 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 375) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1cn(c2ccccc2)nc1c1ccc(F)cc1) `ZINC001435196757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435196757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435196757 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1cn(c2ccccc2)nc1c1ccc(F)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.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 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: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 20, 20, 50, 50, 50, 50, 50, 50, 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435196757 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435196757 Building ZINC001435213847 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435213847 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/376 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/376' -> `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](Cc1ccccc1)c1ccccc1F) `ZINC001435213847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435213847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001435213847 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)c1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 9, 9, 19, 19, 19, 19, 19, 19, 9, 19, 19, 14, 19, 19, 19, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 6, 19, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 132 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/377 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/377' -> `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](Cc1ccccc1)c1ccccc1F) `ZINC001435213847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435213847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001435213847 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)c1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7] 0 hydrogens 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, 7, 8, 8, 4, 4, 1, 1, 1, 1, 4, 4, 4, 7, 7, 20, 20, 20, 20, 20, 20, 7, 16, 16, 7, 16, 16, 16, 4, 4, 4, 8, 8, 7, 8, 8, 4, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20, 16, 16, 12, 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, 53, 54, 55, 56]) total number of confs: 141 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435213847 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847 Building ZINC001435213847 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435213847 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 376) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)c1ccccc1F) `ZINC001435213847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435213847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001435213847 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)c1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 9, 9, 19, 19, 19, 19, 19, 19, 9, 19, 19, 14, 19, 19, 19, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 6, 19, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 132 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 377) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)c1ccccc1F) `ZINC001435213847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435213847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001435213847 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)c1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7] 0 hydrogens 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, 7, 8, 8, 4, 4, 1, 1, 1, 1, 4, 4, 4, 7, 7, 20, 20, 20, 20, 20, 20, 7, 16, 16, 7, 16, 16, 16, 4, 4, 4, 8, 8, 7, 8, 8, 4, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20, 16, 16, 12, 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, 53, 54, 55, 56]) total number of confs: 141 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435213847 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213847 Building ZINC001435213848 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435213848 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/378 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/378' -> `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](Cc1ccccc1)c1ccccc1F) `ZINC001435213848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435213848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001435213848 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](Cc1ccccc1)c1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7] 0 hydrogens 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, 3, 3, 3, 6, 6, 19, 19, 19, 19, 19, 19, 6, 15, 15, 11, 15, 15, 15, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4, 3, 19, 19, 19, 19, 19, 19, 19, 15, 15, 14, 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]) total number of confs: 137 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/379 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/379' -> `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](Cc1ccccc1)c1ccccc1F) `ZINC001435213848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435213848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001435213848 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](Cc1ccccc1)c1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 9, 9, 20, 20, 20, 20, 20, 20, 9, 19, 19, 15, 19, 19, 19, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 6, 20, 20, 20, 20, 20, 20, 20, 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]) total number of confs: 133 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435213848 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848 Building ZINC001435213848 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435213848 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 378) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](Cc1ccccc1)c1ccccc1F) `ZINC001435213848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435213848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001435213848 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](Cc1ccccc1)c1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7] 0 hydrogens 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, 3, 3, 3, 6, 6, 19, 19, 19, 19, 19, 19, 6, 15, 15, 11, 15, 15, 15, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4, 3, 19, 19, 19, 19, 19, 19, 19, 15, 15, 14, 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]) total number of confs: 137 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 379) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](Cc1ccccc1)c1ccccc1F) `ZINC001435213848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435213848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001435213848 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](Cc1ccccc1)c1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 9, 9, 20, 20, 20, 20, 20, 20, 9, 19, 19, 15, 19, 19, 19, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 6, 20, 20, 20, 20, 20, 20, 20, 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]) total number of confs: 133 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435213848 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435213848 Building ZINC001435218331 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435218331 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/380 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCSc1ccccc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001435218331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435218331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001435218331 none O=C(NCCCCSc1ccccc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 14, 1, 1, 1, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 12, 16, 16, 37, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 15, 15, 15, 16, 16, 16, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 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: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/381 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCSc1ccccc1Br)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001435218331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435218331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001435218331 none O=C(NCCCCSc1ccccc1Br)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 14, 1, 1, 1, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 12, 16, 16, 37, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 15, 15, 16, 15, 16, 16, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 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: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435218331 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331 Building ZINC001435218331 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435218331 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 380) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCCCCSc1ccccc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001435218331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435218331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001435218331 none O=C(NCCCCSc1ccccc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 14, 1, 1, 1, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 12, 16, 16, 37, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 15, 15, 15, 16, 16, 16, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 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: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 381) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCCCCSc1ccccc1Br)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001435218331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435218331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001435218331 none O=C(NCCCCSc1ccccc1Br)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 14, 1, 1, 1, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 12, 16, 16, 37, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 15, 15, 16, 15, 16, 16, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 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: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435218331 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218331 Building ZINC001435218760 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435218760 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/382 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](COCc1ccccc1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435218760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435218760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435218760 none O=C(N[C@@H](COCc1ccccc1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.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', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens need 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, 5, 5, 15, 24, 41, 42, 42, 41, 42, 42, 5, 5, 5, 5, 5, 5, 1, 1, 1, 5, 5, 5, 5, 5, 3, 15, 15, 41, 41, 42, 42, 42, 42, 42, 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]) total number of confs: 167 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/383 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/383' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](COCc1ccccc1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435218760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435218760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435218760 none O=C(N[C@@H](COCc1ccccc1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.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', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens need 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, 18, 30, 49, 49, 49, 49, 49, 49, 4, 6, 6, 6, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 2, 18, 18, 49, 49, 49, 49, 49, 49, 49, 6, 6, 6, 6, 6, 4, 4] 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]) total number of confs: 191 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435218760 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760 Building ZINC001435218760 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435218760 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 382) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H](COCc1ccccc1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435218760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435218760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435218760 none O=C(N[C@@H](COCc1ccccc1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.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', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens need 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, 5, 5, 15, 24, 41, 42, 42, 41, 42, 42, 5, 5, 5, 5, 5, 5, 1, 1, 1, 5, 5, 5, 5, 5, 3, 15, 15, 41, 41, 42, 42, 42, 42, 42, 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]) total number of confs: 167 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 383) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H](COCc1ccccc1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435218760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435218760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435218760 none O=C(N[C@@H](COCc1ccccc1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.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', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens need 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, 18, 30, 49, 49, 49, 49, 49, 49, 4, 6, 6, 6, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 2, 18, 18, 49, 49, 49, 49, 49, 49, 49, 6, 6, 6, 6, 6, 4, 4] 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]) total number of confs: 191 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435218760 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218760 Building ZINC001435218762 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435218762 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/384 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](COCc1ccccc1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435218762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435218762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435218762 none O=C(N[C@H](COCc1ccccc1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.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', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens need 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, 18, 30, 48, 49, 49, 48, 49, 49, 4, 6, 6, 4, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 2, 18, 18, 48, 48, 49, 49, 48, 49, 49, 6, 6, 4, 6, 6, 4, 4] 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]) total number of confs: 196 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/385 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/385' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](COCc1ccccc1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435218762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435218762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435218762 none O=C(N[C@H](COCc1ccccc1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.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', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens need 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, 5, 5, 17, 25, 41, 42, 42, 41, 42, 42, 5, 8, 8, 5, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 3, 17, 17, 41, 41, 42, 42, 41, 42, 42, 8, 8, 5, 8, 8, 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]) total number of confs: 185 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435218762 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762 Building ZINC001435218762 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435218762 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 384) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@H](COCc1ccccc1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435218762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435218762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435218762 none O=C(N[C@H](COCc1ccccc1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.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', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens need 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, 18, 30, 48, 49, 49, 48, 49, 49, 4, 6, 6, 4, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 2, 18, 18, 48, 48, 49, 49, 48, 49, 49, 6, 6, 4, 6, 6, 4, 4] 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]) total number of confs: 196 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 385) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@H](COCc1ccccc1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435218762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435218762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435218762 none O=C(N[C@H](COCc1ccccc1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.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', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens need 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, 5, 5, 17, 25, 41, 42, 42, 41, 42, 42, 5, 8, 8, 5, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 3, 17, 17, 41, 41, 42, 42, 41, 42, 42, 8, 8, 5, 8, 8, 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]) total number of confs: 185 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435218762 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435218762 Building ZINC001435250111 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435250111 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/386 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001435250111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435250111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001435250111 none CC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['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', 'C.3', 'F', 'F', 'F', 'H', '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, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 19, 19, 4, 19, 19, 19, 19, 19, 19, 4, 4, 6, 6, 6, 6, 8, 8, 8, 8, 8, 6, 6, 6, 3, 4, 4, 4, 19, 19, 4, 19, 4, 4, 4] 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]) total number of confs: 80 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/387 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/387' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001435250111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435250111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001435250111 none CC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['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', 'C.3', 'F', 'F', 'F', 'H', '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, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 19, 19, 4, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 4, 4, 4, 2, 4, 4, 4, 19, 19, 7, 19, 4, 4, 4] 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]) total number of confs: 72 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435250111 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111 Building ZINC001435250111 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435250111 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 386) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001435250111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435250111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001435250111 none CC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['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', 'C.3', 'F', 'F', 'F', 'H', '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, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 19, 19, 4, 19, 19, 19, 19, 19, 19, 4, 4, 6, 6, 6, 6, 8, 8, 8, 8, 8, 6, 6, 6, 3, 4, 4, 4, 19, 19, 4, 19, 4, 4, 4] 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]) total number of confs: 80 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 387) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001435250111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435250111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001435250111 none CC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['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', 'C.3', 'F', 'F', 'F', 'H', '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, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 19, 19, 4, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 4, 4, 4, 2, 4, 4, 4, 19, 19, 7, 19, 4, 4, 4] 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]) total number of confs: 72 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435250111 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250111 Building ZINC001435250112 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435250112 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/388 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001435250112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435250112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001435250112 none CC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['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', 'C.3', 'F', 'F', 'F', 'H', '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, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 4, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 4, 4, 4, 2, 4, 4, 4, 18, 18, 4, 18, 4, 4, 4] 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]) total number of confs: 64 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/389 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/389' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001435250112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435250112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001435250112 none CC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['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', 'C.3', 'F', 'F', 'F', 'H', '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, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 19, 19, 4, 19, 19, 19, 19, 19, 19, 4, 4, 6, 6, 6, 6, 8, 8, 8, 8, 8, 6, 6, 6, 3, 4, 4, 4, 19, 19, 8, 19, 4, 4, 4] 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]) total number of confs: 88 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435250112 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112 Building ZINC001435250112 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435250112 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 388) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001435250112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435250112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001435250112 none CC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['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', 'C.3', 'F', 'F', 'F', 'H', '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, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 4, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 4, 4, 4, 2, 4, 4, 4, 18, 18, 4, 18, 4, 4, 4] 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]) total number of confs: 64 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 389) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F) `ZINC001435250112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435250112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001435250112 none CC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['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', 'C.3', 'F', 'F', 'F', 'H', '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, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 19, 19, 4, 19, 19, 19, 19, 19, 19, 4, 4, 6, 6, 6, 6, 8, 8, 8, 8, 8, 6, 6, 6, 3, 4, 4, 4, 19, 19, 8, 19, 4, 4, 4] 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]) total number of confs: 88 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435250112 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435250112 Building ZINC001435251037 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435251037 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/390 `/scratch/xiaobo/182395/xbh-8058088.34/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)NC[C@H](C)c1cccc(C)c1) `ZINC001435251037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435251037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435251037 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)c1cccc(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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type 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, 5, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 8, 8, 8, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/391 `/scratch/xiaobo/182395/xbh-8058088.34/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)NC[C@H](C)c1cccc(C)c1) `ZINC001435251037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435251037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435251037 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)c1cccc(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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type 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, 5, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 9, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 9, 9, 9, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435251037 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037 Building ZINC001435251037 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435251037 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 390) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)NC[C@H](C)c1cccc(C)c1) `ZINC001435251037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435251037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435251037 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](C)c1cccc(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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type 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, 5, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 8, 8, 8, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 391) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)NC[C@H](C)c1cccc(C)c1) `ZINC001435251037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435251037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435251037 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](C)c1cccc(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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type 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, 5, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 9, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 9, 9, 9, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435251037 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251037 Building ZINC001435251046 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435251046 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/392 `/scratch/xiaobo/182395/xbh-8058088.34/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)NC[C@@H](C)c1cccc(C)c1) `ZINC001435251046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435251046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435251046 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)c1cccc(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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type 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, 5, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 9, 10, 10, 10, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 9, 9, 10, 10, 10, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/393 `/scratch/xiaobo/182395/xbh-8058088.34/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)NC[C@@H](C)c1cccc(C)c1) `ZINC001435251046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435251046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435251046 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c1cccc(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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type 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, 5, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 8, 8, 8, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435251046 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046 Building ZINC001435251046 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435251046 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 392) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)NC[C@@H](C)c1cccc(C)c1) `ZINC001435251046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435251046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435251046 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](C)c1cccc(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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type 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, 5, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 9, 10, 10, 10, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 9, 9, 10, 10, 10, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 393) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)NC[C@@H](C)c1cccc(C)c1) `ZINC001435251046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435251046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435251046 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c1cccc(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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type 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, 5, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 8, 8, 8, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435251046 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251046 Building ZINC001435251912 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435251912 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/394 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccccc2Br)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435251912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435251912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001435251912 none O=C(NCC1(c2ccccc2Br)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 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] 0 hydrogens need 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, 14, 45, 47, 47, 45, 47, 47, 47, 45, 45, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 14, 14, 47, 47, 47, 47, 45, 45, 45, 45, 3, 1, 3] 50 rigid atoms, others: [1, 14, 15, 16] 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]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/395 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/395' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccccc2Br)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435251912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435251912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001435251912 none O=C(NCC1(c2ccccc2Br)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 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] 0 hydrogens 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, 16, 42, 46, 46, 42, 46, 46, 46, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 16, 16, 46, 46, 46, 46, 42, 42, 42, 42, 3, 1, 3] 50 rigid atoms, others: [1, 14, 15, 16] 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]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435251912 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912 Building ZINC001435251912 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435251912 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 394) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCC1(c2ccccc2Br)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435251912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435251912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001435251912 none O=C(NCC1(c2ccccc2Br)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 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] 0 hydrogens need 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, 14, 45, 47, 47, 45, 47, 47, 47, 45, 45, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 14, 14, 47, 47, 47, 47, 45, 45, 45, 45, 3, 1, 3] 50 rigid atoms, others: [1, 14, 15, 16] 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]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 395) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCC1(c2ccccc2Br)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435251912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435251912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001435251912 none O=C(NCC1(c2ccccc2Br)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 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] 0 hydrogens 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, 16, 42, 46, 46, 42, 46, 46, 46, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 16, 16, 46, 46, 46, 46, 42, 42, 42, 42, 3, 1, 3] 50 rigid atoms, others: [1, 14, 15, 16] 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]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435251912 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435251912 Building ZINC001435256653 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435256653 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/396 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(Oc2ncccc2CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001435256653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435256653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001435256653 none COc1cccc(Oc2ncccc2CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)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.ar', 'C.ar', 'C.ar', 'Cl', '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: [5, 12, 1, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 31, 23, 23, 23, 23, 23, 23, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 11, 11, 2, 2, 1, 2, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/397 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/397' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(Oc2ncccc2CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001435256653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435256653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001435256653 none COc1cccc(Oc2ncccc2CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)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.ar', 'C.ar', 'C.ar', 'Cl', '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: [5, 12, 1, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 23, 23, 23, 23, 23, 23, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 11, 11, 2, 2, 1, 2, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435256653 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653 Building ZINC001435256653 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435256653 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 396) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/396: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2cc(Cl)cc(Cl)c2)c1) `ZINC001435256653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435256653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001435256653 none COc1cccc(Oc2ncccc2CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)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.ar', 'C.ar', 'C.ar', 'Cl', '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: [5, 12, 1, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 31, 23, 23, 23, 23, 23, 23, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 11, 11, 2, 2, 1, 2, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 397) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/397: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2cc(Cl)cc(Cl)c2)c1) `ZINC001435256653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435256653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001435256653 none COc1cccc(Oc2ncccc2CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)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.ar', 'C.ar', 'C.ar', 'Cl', '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: [5, 12, 1, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 23, 23, 23, 23, 23, 23, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 11, 11, 2, 2, 1, 2, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435256653 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435256653 Building ZINC001435268519 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435268519 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/398 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC2(c3ccc(Br)cc3)CCCCC2)cn1) `ZINC001435268519.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435268519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435268519 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC2(c3ccc(Br)cc3)CCCCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 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, 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, 2, 2, 2, 15, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 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: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/399 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC2(c3ccc(Br)cc3)CCCCC2)cn1) `ZINC001435268519.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435268519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435268519 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC2(c3ccc(Br)cc3)CCCCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 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, 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: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 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: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435268519 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519 Building ZINC001435268519 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435268519 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 398) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC2(c3ccc(Br)cc3)CCCCC2)cn1) `ZINC001435268519.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435268519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435268519 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC2(c3ccc(Br)cc3)CCCCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 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, 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, 2, 2, 2, 15, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 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: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 399) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC2(c3ccc(Br)cc3)CCCCC2)cn1) `ZINC001435268519.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435268519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435268519 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC2(c3ccc(Br)cc3)CCCCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 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, 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: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 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: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435268519 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435268519 Building ZINC001435322329 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435322329 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/400 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(OC(C)C)c2)cc1Cl) `ZINC001435322329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435322329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435322329 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(OC(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', 'Br', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 17, 26, 26, 7, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 26, 26, 26, 26, 26, 26, 26, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/401 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/401' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(OC(C)C)c2)cc1Cl) `ZINC001435322329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435322329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435322329 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(OC(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', 'Br', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 17, 27, 27, 7, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 27, 27, 27, 27, 27, 27, 27, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435322329 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329 Building ZINC001435322329 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435322329 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 400) grep: /scratch/xiaobo/182395/xbh-8058088.34/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([C@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(OC(C)C)c2)cc1Cl) `ZINC001435322329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435322329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435322329 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(OC(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', 'Br', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 17, 26, 26, 7, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 26, 26, 26, 26, 26, 26, 26, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 401) grep: /scratch/xiaobo/182395/xbh-8058088.34/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([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(OC(C)C)c2)cc1Cl) `ZINC001435322329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435322329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435322329 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(OC(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', 'Br', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 17, 27, 27, 7, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 27, 27, 27, 27, 27, 27, 27, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435322329 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435322329 Building ZINC001435344294 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435344294 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/402 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(C(F)(F)F)c2)cc1Cl) `ZINC001435344294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435344294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001435344294 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(C(F)(F)F)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 5, 15, 15, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 14, 14, 14, 8, 14, 14, 14, 14, 14, 14, 6, 6, 6, 12, 12, 12, 6, 6, 2, 14, 14, 14, 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/403 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/403' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(C(F)(F)F)c2)cc1Cl) `ZINC001435344294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435344294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001435344294 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(C(F)(F)F)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 5, 15, 15, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 14, 14, 14, 8, 14, 14, 14, 14, 14, 14, 6, 6, 6, 12, 12, 12, 6, 6, 2, 14, 14, 14, 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435344294 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294 Building ZINC001435344294 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435344294 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 402) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(C(F)(F)F)c2)cc1Cl) `ZINC001435344294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435344294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001435344294 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(C(F)(F)F)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 5, 15, 15, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 14, 14, 14, 8, 14, 14, 14, 14, 14, 14, 6, 6, 6, 12, 12, 12, 6, 6, 2, 14, 14, 14, 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 403) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(C(F)(F)F)c2)cc1Cl) `ZINC001435344294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435344294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001435344294 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(C(F)(F)F)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', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 5, 15, 15, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 14, 14, 14, 8, 14, 14, 14, 14, 14, 14, 6, 6, 6, 12, 12, 12, 6, 6, 2, 14, 14, 14, 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435344294 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435344294 Building ZINC001435367150 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435367150 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/404 `/scratch/xiaobo/182395/xbh-8058088.34/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)N[C@@H](C)[C@@H](C)c1ccccc1) `ZINC001435367150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435367150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435367150 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@@H](C)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', 'C.3', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 7, 7, 7, 12, 12, 12, 15, 15, 12, 15, 15, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 3, 7, 7, 7, 12, 12, 12, 15, 15, 12, 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]) total number of confs: 101 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/405 `/scratch/xiaobo/182395/xbh-8058088.34/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)N[C@@H](C)[C@@H](C)c1ccccc1) `ZINC001435367150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435367150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435367150 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@@H](C)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', 'C.3', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 1, 3, 3, 3, 8, 8, 8, 12, 12, 12, 14, 14, 12, 14, 14, 2, 2, 2, 15, 15, 2, 15, 2, 2, 2, 3, 8, 8, 8, 12, 12, 12, 14, 14, 12, 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]) total number of confs: 93 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435367150 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150 Building ZINC001435367150 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435367150 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 404) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)N[C@@H](C)[C@@H](C)c1ccccc1) `ZINC001435367150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435367150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435367150 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@@H](C)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', 'C.3', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 7, 7, 7, 12, 12, 12, 15, 15, 12, 15, 15, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 3, 7, 7, 7, 12, 12, 12, 15, 15, 12, 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]) total number of confs: 101 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 405) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)N[C@@H](C)[C@@H](C)c1ccccc1) `ZINC001435367150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435367150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435367150 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@@H](C)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', 'C.3', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 1, 3, 3, 3, 8, 8, 8, 12, 12, 12, 14, 14, 12, 14, 14, 2, 2, 2, 15, 15, 2, 15, 2, 2, 2, 3, 8, 8, 8, 12, 12, 12, 14, 14, 12, 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]) total number of confs: 93 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435367150 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367150 Building ZINC001435367153 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435367153 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/406 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/406' -> `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)[C@H](C)c1ccccc1) `ZINC001435367153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435367153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435367153 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H](C)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', 'C.3', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 11, 10, 11, 11, 11, 11, 11, 11, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 7, 7, 7, 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, 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/182395/xbh-8058088.34/working/building/ZINC001435367153 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/407 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/407' -> `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)[C@H](C)c1ccccc1) `ZINC001435367153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435367153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435367153 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H](C)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', 'C.3', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 1, 2, 2, 2, 7, 7, 7, 14, 13, 14, 15, 15, 14, 15, 15, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 2, 7, 7, 7, 14, 14, 14, 15, 15, 14, 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]) total number of confs: 95 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435367153 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153 Building ZINC001435367153 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435367153 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 406) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H](C)c1ccccc1) `ZINC001435367153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435367153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435367153 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H](C)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', 'C.3', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 11, 10, 11, 11, 11, 11, 11, 11, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 7, 7, 7, 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, 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/182395/xbh-8058088.34/working/building/ZINC001435367153 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 407) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H](C)c1ccccc1) `ZINC001435367153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435367153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435367153 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H](C)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', 'C.3', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 1, 2, 2, 2, 7, 7, 7, 14, 13, 14, 15, 15, 14, 15, 15, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 2, 7, 7, 7, 14, 14, 14, 15, 15, 14, 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]) total number of confs: 95 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435367153 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367153 Building ZINC001435367155 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435367155 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/408 `/scratch/xiaobo/182395/xbh-8058088.34/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)N[C@H](C)[C@@H](C)c1ccccc1) `ZINC001435367155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435367155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435367155 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H](C)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', 'C.3', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 1, 2, 2, 2, 7, 7, 7, 12, 11, 12, 13, 13, 12, 13, 13, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 2, 7, 7, 7, 12, 12, 12, 13, 13, 12, 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]) total number of confs: 83 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/409 `/scratch/xiaobo/182395/xbh-8058088.34/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)N[C@H](C)[C@@H](C)c1ccccc1) `ZINC001435367155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435367155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435367155 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H](C)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', 'C.3', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 11, 10, 11, 11, 11, 11, 11, 11, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 7, 7, 7, 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, 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/182395/xbh-8058088.34/working/building/ZINC001435367155 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435367155 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155 Building ZINC001435367155 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435367155 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 408) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)N[C@H](C)[C@@H](C)c1ccccc1) `ZINC001435367155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435367155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435367155 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H](C)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', 'C.3', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 1, 2, 2, 2, 7, 7, 7, 12, 11, 12, 13, 13, 12, 13, 13, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 2, 7, 7, 7, 12, 12, 12, 13, 13, 12, 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]) total number of confs: 83 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 409) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)N[C@H](C)[C@@H](C)c1ccccc1) `ZINC001435367155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435367155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435367155 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H](C)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', 'C.3', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 11, 10, 11, 11, 11, 11, 11, 11, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 7, 7, 7, 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, 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/182395/xbh-8058088.34/working/building/ZINC001435367155 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435367155 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367155 Building ZINC001435367157 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435367157 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/410 `/scratch/xiaobo/182395/xbh-8058088.34/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)N[C@H](C)[C@H](C)c1ccccc1) `ZINC001435367157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435367157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435367157 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H](C)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', 'C.3', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 1, 2, 2, 2, 7, 7, 7, 11, 11, 11, 13, 13, 11, 13, 13, 2, 2, 2, 14, 14, 2, 14, 2, 2, 2, 2, 7, 7, 7, 11, 11, 11, 13, 13, 11, 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]) total number of confs: 89 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/411 `/scratch/xiaobo/182395/xbh-8058088.34/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)N[C@H](C)[C@H](C)c1ccccc1) `ZINC001435367157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435367157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435367157 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H](C)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', 'C.3', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 7, 7, 7, 11, 11, 11, 14, 14, 11, 14, 14, 3, 3, 3, 16, 16, 4, 16, 3, 3, 3, 3, 7, 7, 7, 11, 11, 11, 14, 14, 11, 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]) total number of confs: 98 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435367157 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157 Building ZINC001435367157 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435367157 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 410) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)N[C@H](C)[C@H](C)c1ccccc1) `ZINC001435367157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435367157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435367157 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H](C)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', 'C.3', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 1, 2, 2, 2, 7, 7, 7, 11, 11, 11, 13, 13, 11, 13, 13, 2, 2, 2, 14, 14, 2, 14, 2, 2, 2, 2, 7, 7, 7, 11, 11, 11, 13, 13, 11, 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]) total number of confs: 89 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 411) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)N[C@H](C)[C@H](C)c1ccccc1) `ZINC001435367157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435367157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435367157 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H](C)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', 'C.3', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 7, 7, 7, 11, 11, 11, 14, 14, 11, 14, 14, 3, 3, 3, 16, 16, 4, 16, 3, 3, 3, 3, 7, 7, 7, 11, 11, 11, 14, 14, 11, 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]) total number of confs: 98 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435367157 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435367157 Building ZINC001435375266 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435375266 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/412 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC(=O)N(Cc2ccccc2)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001435375266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435375266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001435375266 none C[C@H]1CC(=O)N(Cc2ccccc2)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 6, 6, 6, 6, 6, 20, 23, 23, 20, 23, 23, 6, 6, 6, 6, 6, 6, 6, 3, 6, 1, 1, 1, 11, 11, 11, 11, 11, 6, 6, 6, 6, 6, 20, 20, 23, 23, 20, 23, 23, 6, 6, 6, 6, 11, 11] 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]) total number of confs: 97 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/413 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/413' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC(=O)N(Cc2ccccc2)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001435375266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435375266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001435375266 none C[C@H]1CC(=O)N(Cc2ccccc2)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 8, 8, 8, 8, 25, 27, 27, 25, 27, 27, 8, 8, 8, 8, 8, 8, 6, 2, 6, 1, 1, 1, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 25, 25, 27, 27, 25, 27, 27, 8, 8, 8, 8, 9, 9] 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]) total number of confs: 111 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435375266 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266 Building ZINC001435375266 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435375266 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 412) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@H]1CC(=O)N(Cc2ccccc2)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001435375266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435375266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001435375266 none C[C@H]1CC(=O)N(Cc2ccccc2)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 6, 6, 6, 6, 6, 20, 23, 23, 20, 23, 23, 6, 6, 6, 6, 6, 6, 6, 3, 6, 1, 1, 1, 11, 11, 11, 11, 11, 6, 6, 6, 6, 6, 20, 20, 23, 23, 20, 23, 23, 6, 6, 6, 6, 11, 11] 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]) total number of confs: 97 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 413) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@H]1CC(=O)N(Cc2ccccc2)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001435375266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435375266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001435375266 none C[C@H]1CC(=O)N(Cc2ccccc2)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 8, 8, 8, 8, 25, 27, 27, 25, 27, 27, 8, 8, 8, 8, 8, 8, 6, 2, 6, 1, 1, 1, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 25, 25, 27, 27, 25, 27, 27, 8, 8, 8, 8, 9, 9] 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]) total number of confs: 111 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435375266 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375266 Building ZINC001435375272 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435375272 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/414 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC(=O)N(Cc2ccccc2)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001435375272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435375272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001435375272 none C[C@@H]1CC(=O)N(Cc2ccccc2)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 11, 11, 29, 30, 30, 30, 30, 30, 11, 11, 11, 11, 11, 11, 10, 2, 10, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 29, 29, 30, 30, 30, 30, 30, 11, 11, 11, 11, 6, 6] 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]) total number of confs: 117 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/415 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/415' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC(=O)N(Cc2ccccc2)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001435375272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435375272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001435375272 none C[C@@H]1CC(=O)N(Cc2ccccc2)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 25, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 3, 7, 1, 1, 1, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 25, 25, 26, 26, 26, 26, 26, 7, 7, 7, 7, 9, 9] 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]) total number of confs: 104 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435375272 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272 Building ZINC001435375272 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435375272 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 414) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@H]1CC(=O)N(Cc2ccccc2)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001435375272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435375272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001435375272 none C[C@@H]1CC(=O)N(Cc2ccccc2)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 11, 11, 29, 30, 30, 30, 30, 30, 11, 11, 11, 11, 11, 11, 10, 2, 10, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 29, 29, 30, 30, 30, 30, 30, 11, 11, 11, 11, 6, 6] 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]) total number of confs: 117 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 415) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@H]1CC(=O)N(Cc2ccccc2)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001435375272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435375272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001435375272 none C[C@@H]1CC(=O)N(Cc2ccccc2)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 25, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 3, 7, 1, 1, 1, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 25, 25, 26, 26, 26, 26, 26, 7, 7, 7, 7, 9, 9] 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]) total number of confs: 104 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435375272 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435375272 Building ZINC001435376823 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435376823 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/416 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2N(Cc2ccccc2)C(=O)C[C@H]1C) `ZINC001435376823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435376823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435376823 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2N(Cc2ccccc2)C(=O)C[C@H]1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 7, 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, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 27, 29, 29, 27, 29, 29, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 27, 27, 29, 29, 27, 29, 29, 10, 10, 10, 10, 10] 31 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]) total number of confs: 109 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/417 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/417' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1c2ccccc2N(Cc2ccccc2)C(=O)C[C@H]1C) `ZINC001435376823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435376823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435376823 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1c2ccccc2N(Cc2ccccc2)C(=O)C[C@H]1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 7, 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, 9, 8, 10, 11, 6, 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, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 33, 33, 33, 33, 33, 33, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 33, 33, 33, 33, 33, 33, 33, 11, 11, 11, 11, 11] 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, 50, 51, 52, 53, 54]) total number of confs: 123 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435376823 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823 Building ZINC001435376823 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435376823 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 416) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2N(Cc2ccccc2)C(=O)C[C@H]1C) `ZINC001435376823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435376823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435376823 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2N(Cc2ccccc2)C(=O)C[C@H]1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 7, 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, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 27, 29, 29, 27, 29, 29, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 27, 27, 29, 29, 27, 29, 29, 10, 10, 10, 10, 10] 31 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]) total number of confs: 109 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 417) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1c2ccccc2N(Cc2ccccc2)C(=O)C[C@H]1C) `ZINC001435376823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435376823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435376823 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1c2ccccc2N(Cc2ccccc2)C(=O)C[C@H]1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 7, 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, 9, 8, 10, 11, 6, 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, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 33, 33, 33, 33, 33, 33, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 33, 33, 33, 33, 33, 33, 33, 11, 11, 11, 11, 11] 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, 50, 51, 52, 53, 54]) total number of confs: 123 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435376823 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376823 Building ZINC001435376824 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435376824 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/418 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2N(Cc2ccccc2)C(=O)C[C@@H]1C) `ZINC001435376824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435376824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435376824 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2N(Cc2ccccc2)C(=O)C[C@@H]1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 7, 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, 9, 8, 10, 11, 6, 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, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 25, 27, 27, 25, 27, 27, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 25, 25, 27, 27, 27, 27, 27, 7, 7, 7, 7, 7] 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, 50, 51, 52, 53, 54]) total number of confs: 109 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/419 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/419' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1c2ccccc2N(Cc2ccccc2)C(=O)C[C@@H]1C) `ZINC001435376824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435376824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435376824 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1c2ccccc2N(Cc2ccccc2)C(=O)C[C@@H]1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 7, 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, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 17, 20, 20, 17, 20, 20, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 17, 17, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7] 22 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: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435376824 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824 Building ZINC001435376824 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435376824 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 418) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2N(Cc2ccccc2)C(=O)C[C@@H]1C) `ZINC001435376824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435376824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435376824 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2N(Cc2ccccc2)C(=O)C[C@@H]1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 7, 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, 9, 8, 10, 11, 6, 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, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 25, 27, 27, 25, 27, 27, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 25, 25, 27, 27, 27, 27, 27, 7, 7, 7, 7, 7] 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, 50, 51, 52, 53, 54]) total number of confs: 109 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 419) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1c2ccccc2N(Cc2ccccc2)C(=O)C[C@@H]1C) `ZINC001435376824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435376824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435376824 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1c2ccccc2N(Cc2ccccc2)C(=O)C[C@@H]1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 7, 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, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 17, 20, 20, 17, 20, 20, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 17, 17, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7] 22 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: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435376824 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435376824 Building ZINC001435413967 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435413967 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/420 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cc(F)ccc1F)C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435413967.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435413967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001435413967 none O=C(N(Cc1cc(F)ccc1F)C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 15, 1, 1, 1, 15, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [4, 1, 4, 7, 16, 24, 24, 24, 24, 24, 24, 24, 8, 13, 13, 13, 13, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 24, 24, 24, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/421 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/421' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cc(F)ccc1F)C1CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435413967.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435413967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001435413967 none O=C(N(Cc1cc(F)ccc1F)C1CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 15, 1, 1, 1, 15, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [4, 1, 4, 7, 16, 25, 25, 25, 25, 25, 25, 25, 8, 14, 14, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 25, 25, 25, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435413967 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967 Building ZINC001435413967 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435413967 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 420) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N(Cc1cc(F)ccc1F)C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435413967.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435413967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001435413967 none O=C(N(Cc1cc(F)ccc1F)C1CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 15, 1, 1, 1, 15, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [4, 1, 4, 7, 16, 24, 24, 24, 24, 24, 24, 24, 8, 13, 13, 13, 13, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 24, 24, 24, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 421) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N(Cc1cc(F)ccc1F)C1CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435413967.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435413967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001435413967 none O=C(N(Cc1cc(F)ccc1F)C1CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 15, 1, 1, 1, 15, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [4, 1, 4, 7, 16, 25, 25, 25, 25, 25, 25, 25, 8, 14, 14, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 25, 25, 25, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435413967 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435413967 Building ZINC001435463248 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435463248 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/422 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2Br)CC(C)C)cc1Cl) `ZINC001435463248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435463248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435463248 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2Br)CC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 17, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 4, 6, 11, 16, 16, 11, 16, 16, 16, 6, 7, 7, 7, 6, 6, 6, 10, 10, 10, 6, 6, 11, 11, 16, 16, 13, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 101 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/423 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/423' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2Br)CC(C)C)cc1Cl) `ZINC001435463248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435463248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435463248 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2Br)CC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 17, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 15, 15, 12, 15, 15, 15, 3, 4, 5, 5, 4, 4, 4, 8, 8, 8, 4, 4, 8, 8, 15, 15, 12, 15, 4, 4, 5, 5, 5, 5, 5, 5, 5, 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]) total number of confs: 83 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435463248 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248 Building ZINC001435463248 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435463248 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 422) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)N(Cc2ccccc2Br)CC(C)C)cc1Cl) `ZINC001435463248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435463248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435463248 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2Br)CC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 17, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 4, 6, 11, 16, 16, 11, 16, 16, 16, 6, 7, 7, 7, 6, 6, 6, 10, 10, 10, 6, 6, 11, 11, 16, 16, 13, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 101 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 423) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)N(Cc2ccccc2Br)CC(C)C)cc1Cl) `ZINC001435463248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435463248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435463248 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2Br)CC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 17, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 15, 15, 12, 15, 15, 15, 3, 4, 5, 5, 4, 4, 4, 8, 8, 8, 4, 4, 8, 8, 15, 15, 12, 15, 4, 4, 5, 5, 5, 5, 5, 5, 5, 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]) total number of confs: 83 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435463248 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435463248 Building ZINC001435469589 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435469589 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/424 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/424' -> `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(Cl)c(Br)c1) `ZINC001435469589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435469589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001435469589 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 16, 1, 17, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 28, 28, 17, 28, 28, 28, 28, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 5, 28, 28, 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]) total number of confs: 121 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/425 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/425' -> `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(Cl)c(Br)c1) `ZINC001435469589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435469589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001435469589 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 16, 1, 17, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 5, 29, 29, 29] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 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: 68 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435469589 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589 Building ZINC001435469589 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435469589 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 424) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(Br)c1) `ZINC001435469589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435469589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001435469589 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 16, 1, 17, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 28, 28, 17, 28, 28, 28, 28, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 5, 28, 28, 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]) total number of confs: 121 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 425) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(Br)c1) `ZINC001435469589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435469589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001435469589 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 16, 1, 17, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 5, 29, 29, 29] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 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: 68 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435469589 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435469589 Building ZINC001435476704 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435476704 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/426 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)c2ccccc2c1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001435476704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435476704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435476704 none Cc1cc(Br)c2ccccc2c1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', '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, 1, 1, 1, 1, 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: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 18, 18, 11, 18, 18, 11, 18, 18, 18, 18, 18, 18, 18, 18, 4, 11, 18, 18, 11, 18, 18, 11] 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/427 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/427' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)c2ccccc2c1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001435476704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435476704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435476704 none Cc1cc(Br)c2ccccc2c1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', '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, 1, 1, 1, 1, 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: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 18, 18, 11, 18, 18, 11, 18, 18, 18, 18, 18, 18, 18, 18, 4, 11, 18, 18, 18, 18, 18, 11] 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435476704 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704 Building ZINC001435476704 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435476704 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 426) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(Br)c2ccccc2c1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001435476704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435476704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435476704 none Cc1cc(Br)c2ccccc2c1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', '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, 1, 1, 1, 1, 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: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 18, 18, 11, 18, 18, 11, 18, 18, 18, 18, 18, 18, 18, 18, 4, 11, 18, 18, 11, 18, 18, 11] 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 427) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(Br)c2ccccc2c1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001435476704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435476704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435476704 none Cc1cc(Br)c2ccccc2c1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', '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, 1, 1, 1, 1, 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: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 18, 18, 11, 18, 18, 11, 18, 18, 18, 18, 18, 18, 18, 18, 4, 11, 18, 18, 18, 18, 18, 11] 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435476704 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435476704 Building ZINC001435483207 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435483207 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/428 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/428' -> `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(Cl)cc1Br) `ZINC001435483207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435483207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001435483207 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'Cl', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 16, 1, 1, 17, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 12, 12, 4, 4, 1, 1, 1, 1, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 9, 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]) total number of confs: 81 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/429 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/429' -> `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(Cl)cc1Br) `ZINC001435483207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435483207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001435483207 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'Cl', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 16, 1, 1, 17, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 5, 14, 14, 5, 5, 1, 1, 1, 1, 8, 8, 8, 31, 31, 11, 21, 31, 31, 31, 5, 5, 5, 14, 14, 8, 14, 14, 5, 5, 5, 8, 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]) total number of confs: 138 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435483207 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207 Building ZINC001435483207 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435483207 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 428) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1Br) `ZINC001435483207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435483207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001435483207 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'Cl', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 16, 1, 1, 17, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 12, 12, 4, 4, 1, 1, 1, 1, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 9, 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]) total number of confs: 81 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 429) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1Br) `ZINC001435483207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435483207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001435483207 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'Cl', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 16, 1, 1, 17, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 5, 14, 14, 5, 5, 1, 1, 1, 1, 8, 8, 8, 31, 31, 11, 21, 31, 31, 31, 5, 5, 5, 14, 14, 8, 14, 14, 5, 5, 5, 8, 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]) total number of confs: 138 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435483207 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435483207 Building ZINC001435497909 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435497909 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/430 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)(F)C(F)(F)F)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435497909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435497909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001435497909 none O=C(Nc1ccc(OC(F)(F)C(F)(F)F)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 35, 35, 35, 35, 36, 35, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4, 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/431 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/431' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)(F)C(F)(F)F)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435497909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435497909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001435497909 none O=C(Nc1ccc(OC(F)(F)C(F)(F)F)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 34, 34, 34, 34, 34, 34, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4, 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435497909 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909 Building ZINC001435497909 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435497909 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 430) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1ccc(OC(F)(F)C(F)(F)F)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435497909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435497909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001435497909 none O=C(Nc1ccc(OC(F)(F)C(F)(F)F)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 35, 35, 35, 35, 36, 35, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4, 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 431) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1ccc(OC(F)(F)C(F)(F)F)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435497909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435497909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001435497909 none O=C(Nc1ccc(OC(F)(F)C(F)(F)F)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 34, 34, 34, 34, 34, 34, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4, 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435497909 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435497909 Building ZINC001435515553 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435515553 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/432 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl) `ZINC001435515553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435515553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435515553 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](Oc3ccc(Cl)c(Cl)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', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 4, 4, 4, 4, 8, 27, 27, 24, 27, 27, 27, 27, 4, 2, 2, 2, 4, 4, 4, 2, 2, 4, 4, 4, 4, 27, 27, 27, 4, 4, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/433 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/433' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl) `ZINC001435515553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435515553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435515553 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](Oc3ccc(Cl)c(Cl)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', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 10, 30, 30, 22, 30, 30, 30, 30, 4, 2, 2, 2, 5, 5, 5, 2, 2, 4, 4, 4, 4, 30, 30, 30, 4, 4, 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435515553 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553 Building ZINC001435515553 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435515553 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 432) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)N2CC[C@@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl) `ZINC001435515553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435515553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435515553 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](Oc3ccc(Cl)c(Cl)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', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 4, 4, 4, 4, 8, 27, 27, 24, 27, 27, 27, 27, 4, 2, 2, 2, 4, 4, 4, 2, 2, 4, 4, 4, 4, 27, 27, 27, 4, 4, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 433) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)N2CC[C@@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl) `ZINC001435515553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435515553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435515553 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](Oc3ccc(Cl)c(Cl)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', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 10, 30, 30, 22, 30, 30, 30, 30, 4, 2, 2, 2, 5, 5, 5, 2, 2, 4, 4, 4, 4, 30, 30, 30, 4, 4, 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435515553 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515553 Building ZINC001435515556 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435515556 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/434 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl) `ZINC001435515556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435515556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435515556 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](Oc3ccc(Cl)c(Cl)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', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 11, 30, 30, 22, 30, 30, 30, 30, 4, 2, 2, 2, 5, 5, 5, 2, 2, 4, 4, 4, 4, 30, 30, 30, 4, 4, 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/435 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/435' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl) `ZINC001435515556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435515556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435515556 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](Oc3ccc(Cl)c(Cl)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', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 4, 4, 4, 4, 8, 28, 28, 17, 28, 28, 28, 28, 4, 2, 2, 2, 4, 4, 4, 2, 2, 4, 4, 4, 4, 28, 28, 28, 4, 4, 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435515556 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556 Building ZINC001435515556 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435515556 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 434) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)N2CC[C@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl) `ZINC001435515556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435515556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435515556 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](Oc3ccc(Cl)c(Cl)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', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 11, 30, 30, 22, 30, 30, 30, 30, 4, 2, 2, 2, 5, 5, 5, 2, 2, 4, 4, 4, 4, 30, 30, 30, 4, 4, 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 435) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)N2CC[C@H](Oc3ccc(Cl)c(Cl)c3)C2)cc1Cl) `ZINC001435515556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435515556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435515556 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](Oc3ccc(Cl)c(Cl)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', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 4, 4, 4, 4, 8, 28, 28, 17, 28, 28, 28, 28, 4, 2, 2, 2, 4, 4, 4, 2, 2, 4, 4, 4, 4, 28, 28, 28, 4, 4, 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435515556 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435515556 Building ZINC001435522304 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435522304 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/436 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(c3nc4cc(F)c(F)cc4[nH]3)cc2)cc1Cl) `ZINC001435522304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435522304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001435522304 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(c3nc4cc(F)c(F)cc4[nH]3)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', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 8, 1, 1, 1, 15, 1, 15, 1, 1, 8, 6, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 1, 1, 1, 3, 3, 3, 9, 9, 3, 3, 18, 29, 29, 30, 35, 33, 35, 29, 29, 18, 17, 9, 9, 6, 6, 6, 14, 14, 14, 6, 6, 3, 9, 9, 29, 29, 9, 9, 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, 40, 41, 42, 43, 44]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/437 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/437' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(c3nc4cc(F)c(F)cc4[nH]3)cc2)cc1Cl) `ZINC001435522304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435522304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001435522304 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(c3nc4cc(F)c(F)cc4[nH]3)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', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 8, 1, 1, 1, 15, 1, 15, 1, 1, 8, 6, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 5, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 6, 6, 6, 14, 14, 14, 6, 6, 3, 8, 8, 25, 25, 8, 8, 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, 40, 41, 42, 43, 44]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435522304 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304 Building ZINC001435522304 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435522304 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 436) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)Nc2ccc(c3nc4cc(F)c(F)cc4[nH]3)cc2)cc1Cl) `ZINC001435522304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435522304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001435522304 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(c3nc4cc(F)c(F)cc4[nH]3)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', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 8, 1, 1, 1, 15, 1, 15, 1, 1, 8, 6, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 1, 1, 1, 3, 3, 3, 9, 9, 3, 3, 18, 29, 29, 30, 35, 33, 35, 29, 29, 18, 17, 9, 9, 6, 6, 6, 14, 14, 14, 6, 6, 3, 9, 9, 29, 29, 9, 9, 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, 40, 41, 42, 43, 44]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 437) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)Nc2ccc(c3nc4cc(F)c(F)cc4[nH]3)cc2)cc1Cl) `ZINC001435522304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435522304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001435522304 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(c3nc4cc(F)c(F)cc4[nH]3)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', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 8, 1, 1, 1, 15, 1, 15, 1, 1, 8, 6, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 5, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 6, 6, 6, 14, 14, 14, 6, 6, 3, 8, 8, 25, 25, 8, 8, 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, 40, 41, 42, 43, 44]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435522304 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435522304 Building ZINC001435558465 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435558465 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/438 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/438' -> `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](COc1c(C)cccc1C)C(C)(C)C) `ZINC001435558465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435558465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001435558465 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](COc1c(C)cccc1C)C(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.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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 12, 1, 1, 5, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 11, 11, 3, 3, 1, 1, 1, 1, 4, 4, 4, 9, 9, 23, 35, 35, 35, 35, 35, 35, 35, 35, 9, 10, 10, 10, 3, 3, 3, 11, 11, 6, 11, 11, 3, 3, 3, 4, 23, 23, 35, 35, 35, 35, 35, 35, 35, 35, 35, 10, 10, 10, 10, 10, 10, 10, 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, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 148 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/439 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/439' -> `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](COc1c(C)cccc1C)C(C)(C)C) `ZINC001435558465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435558465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001435558465 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](COc1c(C)cccc1C)C(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.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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 12, 1, 1, 5, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 13, 13, 27, 37, 37, 37, 37, 37, 37, 37, 37, 13, 13, 13, 13, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 5, 27, 27, 37, 37, 37, 37, 37, 37, 37, 37, 37, 13, 13, 13, 13, 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, 62, 63, 64, 65]) total number of confs: 146 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435558465 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465 Building ZINC001435558465 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435558465 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 438) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](COc1c(C)cccc1C)C(C)(C)C) `ZINC001435558465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435558465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001435558465 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](COc1c(C)cccc1C)C(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.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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 12, 1, 1, 5, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 11, 11, 3, 3, 1, 1, 1, 1, 4, 4, 4, 9, 9, 23, 35, 35, 35, 35, 35, 35, 35, 35, 9, 10, 10, 10, 3, 3, 3, 11, 11, 6, 11, 11, 3, 3, 3, 4, 23, 23, 35, 35, 35, 35, 35, 35, 35, 35, 35, 10, 10, 10, 10, 10, 10, 10, 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, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 148 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 439) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](COc1c(C)cccc1C)C(C)(C)C) `ZINC001435558465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435558465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001435558465 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](COc1c(C)cccc1C)C(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.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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 12, 1, 1, 5, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 13, 13, 27, 37, 37, 37, 37, 37, 37, 37, 37, 13, 13, 13, 13, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 5, 27, 27, 37, 37, 37, 37, 37, 37, 37, 37, 37, 13, 13, 13, 13, 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, 62, 63, 64, 65]) total number of confs: 146 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435558465 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558465 Building ZINC001435558466 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435558466 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/440 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/440' -> `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](COc1c(C)cccc1C)C(C)(C)C) `ZINC001435558466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435558466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001435558466 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](COc1c(C)cccc1C)C(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.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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 12, 1, 1, 5, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 13, 13, 26, 37, 37, 37, 37, 37, 37, 37, 37, 13, 14, 14, 14, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 5, 26, 26, 37, 37, 37, 37, 37, 37, 37, 37, 37, 14, 14, 14, 14, 14, 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, 62, 63, 64, 65]) total number of confs: 151 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/441 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/441' -> `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](COc1c(C)cccc1C)C(C)(C)C) `ZINC001435558466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435558466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001435558466 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](COc1c(C)cccc1C)C(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.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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 12, 1, 1, 5, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 9, 9, 23, 36, 36, 36, 36, 36, 36, 36, 36, 9, 10, 10, 10, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 4, 23, 23, 36, 36, 36, 36, 36, 36, 36, 36, 36, 10, 10, 10, 10, 10, 10, 10, 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, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 143 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435558466 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466 Building ZINC001435558466 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435558466 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 440) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](COc1c(C)cccc1C)C(C)(C)C) `ZINC001435558466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435558466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001435558466 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](COc1c(C)cccc1C)C(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.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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 12, 1, 1, 5, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 13, 13, 26, 37, 37, 37, 37, 37, 37, 37, 37, 13, 14, 14, 14, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 5, 26, 26, 37, 37, 37, 37, 37, 37, 37, 37, 37, 14, 14, 14, 14, 14, 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, 62, 63, 64, 65]) total number of confs: 151 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 441) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](COc1c(C)cccc1C)C(C)(C)C) `ZINC001435558466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435558466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001435558466 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](COc1c(C)cccc1C)C(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.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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 12, 1, 1, 5, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 9, 9, 23, 36, 36, 36, 36, 36, 36, 36, 36, 9, 10, 10, 10, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 4, 23, 23, 36, 36, 36, 36, 36, 36, 36, 36, 36, 10, 10, 10, 10, 10, 10, 10, 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, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 143 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435558466 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435558466 Building ZINC001435580738 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435580738 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/442 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(c2cccc(Br)c2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001435580738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435580738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001435580738 none CC1(c2cccc(Br)c2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 17, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 28, 28, 26, 28, 28, 28, 9, 9, 4, 1, 4, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 9, 9, 9, 9, 9, 28, 28, 28, 28, 9, 9, 9, 9, 4, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/443 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/443' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(c2cccc(Br)c2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001435580738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435580738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001435580738 none CC1(c2cccc(Br)c2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 17, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 26, 26, 6, 6, 4, 1, 4, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 6, 6, 6, 6, 6, 26, 26, 26, 26, 6, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435580738 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738 Building ZINC001435580738 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435580738 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 442) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/442: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(c2cccc(Br)c2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001435580738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435580738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001435580738 none CC1(c2cccc(Br)c2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 17, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 28, 28, 26, 28, 28, 28, 9, 9, 4, 1, 4, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 9, 9, 9, 9, 9, 28, 28, 28, 28, 9, 9, 9, 9, 4, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 443) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(c2cccc(Br)c2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001435580738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435580738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001435580738 none CC1(c2cccc(Br)c2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 17, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 26, 26, 6, 6, 4, 1, 4, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 6, 6, 6, 6, 6, 26, 26, 26, 26, 6, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435580738 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435580738 Building ZINC001435584629 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435584629 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/444 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](Cc2nc(C3CCCCCC3)no2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001435584629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435584629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001435584629 none O=C(N1CCC[C@@H](Cc2nc(C3CCCCCC3)no2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', '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', '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, 5, 1, 8, 1, 5, 5, 5, 5, 5, 5, 5, 8, 12, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 2, 2, 2, 2, 2, 6, 22, 22, 22, 50, 50, 50, 50, 50, 50, 22, 22, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1] 50 rigid atoms, others: [0, 1, 2, 54, 53, 22, 23, 24, 25, 26, 27, 28, 29] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/445 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](Cc2nc(C3CCCCCC3)no2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001435584629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435584629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001435584629 none O=C(N1CCC[C@@H](Cc2nc(C3CCCCCC3)no2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', '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', '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, 5, 1, 8, 1, 5, 5, 5, 5, 5, 5, 5, 8, 12, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 2, 2, 2, 2, 2, 4, 17, 17, 17, 41, 41, 41, 41, 41, 41, 17, 17, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 24, 22, 23] set([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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435584629 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629 Building ZINC001435584629 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435584629 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 444) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCC[C@@H](Cc2nc(C3CCCCCC3)no2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001435584629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435584629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001435584629 none O=C(N1CCC[C@@H](Cc2nc(C3CCCCCC3)no2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', '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', '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, 5, 1, 8, 1, 5, 5, 5, 5, 5, 5, 5, 8, 12, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 2, 2, 2, 2, 2, 6, 22, 22, 22, 50, 50, 50, 50, 50, 50, 22, 22, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1] 50 rigid atoms, others: [0, 1, 2, 54, 53, 22, 23, 24, 25, 26, 27, 28, 29] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 445) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCC[C@@H](Cc2nc(C3CCCCCC3)no2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001435584629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435584629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001435584629 none O=C(N1CCC[C@@H](Cc2nc(C3CCCCCC3)no2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', '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', '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, 5, 1, 8, 1, 5, 5, 5, 5, 5, 5, 5, 8, 12, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 2, 2, 2, 2, 2, 4, 17, 17, 17, 41, 41, 41, 41, 41, 41, 17, 17, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 24, 22, 23] set([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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435584629 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584629 Building ZINC001435584633 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435584633 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/446 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](Cc2nc(C3CCCCCC3)no2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001435584633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435584633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001435584633 none O=C(N1CCC[C@H](Cc2nc(C3CCCCCC3)no2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', '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', '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, 5, 1, 8, 1, 5, 5, 5, 5, 5, 5, 5, 8, 12, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 3, 3, 3, 3, 3, 9, 23, 23, 23, 48, 48, 48, 48, 48, 48, 23, 23, 3, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 9, 9, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3, 2, 2] 50 rigid atoms, others: [0, 1, 24, 22, 23] set([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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/447 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/447' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](Cc2nc(C3CCCCCC3)no2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001435584633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435584633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001435584633 none O=C(N1CCC[C@H](Cc2nc(C3CCCCCC3)no2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', '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', '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, 5, 1, 8, 1, 5, 5, 5, 5, 5, 5, 5, 8, 12, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 2, 2, 2, 2, 2, 6, 22, 22, 22, 50, 50, 50, 50, 50, 50, 22, 22, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1] 50 rigid atoms, others: [0, 1, 54, 53, 22, 23, 24, 25, 26, 27, 28, 29] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435584633 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633 Building ZINC001435584633 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435584633 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 446) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/446: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](Cc2nc(C3CCCCCC3)no2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001435584633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435584633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001435584633 none O=C(N1CCC[C@H](Cc2nc(C3CCCCCC3)no2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', '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', '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, 5, 1, 8, 1, 5, 5, 5, 5, 5, 5, 5, 8, 12, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 3, 3, 3, 3, 3, 9, 23, 23, 23, 48, 48, 48, 48, 48, 48, 23, 23, 3, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 9, 9, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3, 2, 2] 50 rigid atoms, others: [0, 1, 24, 22, 23] set([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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 447) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](Cc2nc(C3CCCCCC3)no2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001435584633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435584633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001435584633 none O=C(N1CCC[C@H](Cc2nc(C3CCCCCC3)no2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', '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', '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, 5, 1, 8, 1, 5, 5, 5, 5, 5, 5, 5, 8, 12, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 2, 2, 2, 2, 2, 6, 22, 22, 22, 50, 50, 50, 50, 50, 50, 22, 22, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1] 50 rigid atoms, others: [0, 1, 54, 53, 22, 23, 24, 25, 26, 27, 28, 29] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435584633 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435584633 Building ZINC001435594415 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435594415 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/448 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnn(c2ccccc2Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435594415.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435594415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001435594415 none O=C(Nc1cnn(c2ccccc2Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 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: [4, 1, 4, 4, 13, 13, 13, 13, 39, 39, 14, 39, 39, 39, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 13, 39, 39, 24, 39, 13, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/449 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/449' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnn(c2ccccc2Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435594415.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435594415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001435594415 none O=C(Nc1cnn(c2ccccc2Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 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: [4, 1, 4, 4, 14, 14, 14, 14, 38, 38, 14, 38, 38, 38, 14, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 14, 38, 38, 28, 38, 14, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435594415 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415 Building ZINC001435594415 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435594415 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 448) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cnn(c2ccccc2Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435594415.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435594415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001435594415 none O=C(Nc1cnn(c2ccccc2Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 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: [4, 1, 4, 4, 13, 13, 13, 13, 39, 39, 14, 39, 39, 39, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 13, 39, 39, 24, 39, 13, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 449) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cnn(c2ccccc2Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435594415.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435594415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001435594415 none O=C(Nc1cnn(c2ccccc2Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 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: [4, 1, 4, 4, 14, 14, 14, 14, 38, 38, 14, 38, 38, 38, 14, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 14, 38, 38, 28, 38, 14, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435594415 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435594415 Building ZINC001435637438 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435637438 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/450 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/450' -> `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)NCc1c(C)cccc1C) `ZINC001435637438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435637438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435637438 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1c(C)cccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.3', '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'] dock atom type 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, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 5, 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]) total number of confs: 66 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/451 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/451' -> `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)NCc1c(C)cccc1C) `ZINC001435637438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435637438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435637438 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1c(C)cccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.3', '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'] dock atom type 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, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 4, 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]) total number of confs: 72 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435637438 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438 Building ZINC001435637438 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435637438 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 450) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1c(C)cccc1C) `ZINC001435637438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435637438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435637438 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1c(C)cccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.3', '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'] dock atom type 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, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 5, 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]) total number of confs: 66 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 451) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1c(C)cccc1C) `ZINC001435637438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435637438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435637438 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1c(C)cccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.3', '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'] dock atom type 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, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 4, 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]) total number of confs: 72 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435637438 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435637438 Building ZINC001435662110 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435662110 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/452 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(Br)cc(F)cc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001435662110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435662110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001435662110 none O=C(Nc1c(Br)cc(F)cc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 17, 1, 1, 15, 1, 1, 17, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 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] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 19, 19, 19, 10, 10, 19, 19, 19, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 10, 19, 19, 12, 12, 12, 12, 12, 12, 12, 12, 12] 49 rigid atoms, others: [1, 12, 13, 14] set([0, 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/453 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/453' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(Br)cc(F)cc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001435662110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435662110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001435662110 none O=C(Nc1c(Br)cc(F)cc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 17, 1, 1, 15, 1, 1, 17, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 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] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 20, 20, 20, 17, 20, 20, 20, 20, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 11, 20, 20, 12, 12, 12, 12, 12, 12, 12, 12, 12] 49 rigid atoms, others: [1, 12, 13, 14] set([0, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435662110 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110 Building ZINC001435662110 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435662110 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 452) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1c(Br)cc(F)cc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001435662110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435662110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001435662110 none O=C(Nc1c(Br)cc(F)cc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 17, 1, 1, 15, 1, 1, 17, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 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] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 19, 19, 19, 10, 10, 19, 19, 19, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 10, 19, 19, 12, 12, 12, 12, 12, 12, 12, 12, 12] 49 rigid atoms, others: [1, 12, 13, 14] set([0, 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 453) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1c(Br)cc(F)cc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001435662110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435662110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001435662110 none O=C(Nc1c(Br)cc(F)cc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 17, 1, 1, 15, 1, 1, 17, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 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] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 20, 20, 20, 17, 20, 20, 20, 20, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 11, 20, 20, 12, 12, 12, 12, 12, 12, 12, 12, 12] 49 rigid atoms, others: [1, 12, 13, 14] set([0, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435662110 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662110 Building ZINC001435662158 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435662158 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/454 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1c(Br)cc(F)cc1Br) `ZINC001435662158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435662158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001435662158 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1c(Br)cc(F)cc1Br 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.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 17, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 10, 10, 10, 18, 18, 18, 11, 15, 18, 18, 18, 5, 5, 5, 5, 5, 5, 10, 18, 18] 18 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/455 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1c(Br)cc(F)cc1Br) `ZINC001435662158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435662158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001435662158 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1c(Br)cc(F)cc1Br 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.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 17, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 18, 18, 18, 14, 15, 18, 18, 18, 6, 6, 6, 6, 6, 6, 10, 18, 18] 19 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435662158 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158 Building ZINC001435662158 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435662158 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 454) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1c(Br)cc(F)cc1Br) `ZINC001435662158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435662158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001435662158 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1c(Br)cc(F)cc1Br 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.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 17, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 10, 10, 10, 18, 18, 18, 11, 15, 18, 18, 18, 5, 5, 5, 5, 5, 5, 10, 18, 18] 18 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 455) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1c(Br)cc(F)cc1Br) `ZINC001435662158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435662158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001435662158 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1c(Br)cc(F)cc1Br 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.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 17, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 18, 18, 18, 14, 15, 18, 18, 18, 6, 6, 6, 6, 6, 6, 10, 18, 18] 19 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435662158 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435662158 Building ZINC001435663642 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435663642 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/456 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnn(c2ccccc2)c1C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435663642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435663642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001435663642 none O=C(Nc1cnn(c2ccccc2)c1C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 19, 19, 19, 19, 30, 30, 24, 30, 30, 19, 19, 19, 19, 19, 1, 1, 1, 12, 12, 12, 12, 12, 7, 19, 30, 30, 30, 30, 30, 12, 12] 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/457 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/457' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnn(c2ccccc2)c1C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435663642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435663642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001435663642 none O=C(Nc1cnn(c2ccccc2)c1C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 17, 17, 17, 17, 27, 27, 17, 27, 27, 17, 17, 17, 17, 17, 1, 1, 1, 11, 11, 11, 11, 11, 7, 17, 27, 27, 17, 27, 27, 11, 11] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435663642 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642 Building ZINC001435663642 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435663642 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 456) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cnn(c2ccccc2)c1C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435663642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435663642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001435663642 none O=C(Nc1cnn(c2ccccc2)c1C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 19, 19, 19, 19, 30, 30, 24, 30, 30, 19, 19, 19, 19, 19, 1, 1, 1, 12, 12, 12, 12, 12, 7, 19, 30, 30, 30, 30, 30, 12, 12] 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 457) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cnn(c2ccccc2)c1C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435663642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435663642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001435663642 none O=C(Nc1cnn(c2ccccc2)c1C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 17, 17, 17, 17, 27, 27, 17, 27, 27, 17, 17, 17, 17, 17, 1, 1, 1, 11, 11, 11, 11, 11, 7, 17, 27, 27, 17, 27, 27, 11, 11] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435663642 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435663642 Building ZINC001435683755 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435683755 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/458 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001435683755.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435683755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435683755 none Cc1nn(c2ccccc2)c(C)c1[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 49, 49, 28, 49, 49, 28, 28, 11, 6, 11, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 11, 11, 11, 11, 28, 28, 28, 49, 49, 28, 49, 49, 28, 28, 28, 6, 6, 6, 6, 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, 46]) total number of confs: 181 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/459 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/459' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001435683755.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435683755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435683755 none Cc1nn(c2ccccc2)c(C)c1[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 48, 27, 48, 48, 27, 27, 9, 5, 9, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 9, 9, 9, 9, 27, 27, 27, 48, 48, 28, 48, 48, 27, 27, 27, 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]) total number of confs: 168 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435683755 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755 Building ZINC001435683755 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435683755 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 458) grep: /scratch/xiaobo/182395/xbh-8058088.34/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@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001435683755.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435683755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435683755 none Cc1nn(c2ccccc2)c(C)c1[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 49, 49, 28, 49, 49, 28, 28, 11, 6, 11, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 11, 11, 11, 11, 28, 28, 28, 49, 49, 28, 49, 49, 28, 28, 28, 6, 6, 6, 6, 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, 46]) total number of confs: 181 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 459) grep: /scratch/xiaobo/182395/xbh-8058088.34/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@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001435683755.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435683755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435683755 none Cc1nn(c2ccccc2)c(C)c1[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 48, 27, 48, 48, 27, 27, 9, 5, 9, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 9, 9, 9, 9, 27, 27, 27, 48, 48, 28, 48, 48, 27, 27, 27, 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]) total number of confs: 168 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435683755 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683755 Building ZINC001435683763 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435683763 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/460 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001435683763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435683763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435683763 none Cc1nn(c2ccccc2)c(C)c1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 48, 43, 48, 48, 27, 27, 9, 5, 9, 5, 1, 5, 1, 1, 1, 5, 5, 2, 5, 5, 5, 9, 9, 9, 9, 27, 27, 27, 48, 48, 44, 48, 48, 27, 27, 27, 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]) total number of confs: 127 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/461 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/461' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001435683763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435683763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435683763 none Cc1nn(c2ccccc2)c(C)c1[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 43, 50, 50, 29, 29, 11, 6, 11, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 11, 11, 11, 29, 29, 29, 50, 50, 45, 50, 50, 29, 29, 29, 6, 6, 6, 6, 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, 46]) total number of confs: 137 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435683763 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763 Building ZINC001435683763 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435683763 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 460) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2ccccc2)c(C)c1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001435683763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435683763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435683763 none Cc1nn(c2ccccc2)c(C)c1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 48, 43, 48, 48, 27, 27, 9, 5, 9, 5, 1, 5, 1, 1, 1, 5, 5, 2, 5, 5, 5, 9, 9, 9, 9, 27, 27, 27, 48, 48, 44, 48, 48, 27, 27, 27, 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]) total number of confs: 127 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 461) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2ccccc2)c(C)c1[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001435683763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435683763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001435683763 none Cc1nn(c2ccccc2)c(C)c1[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 43, 50, 50, 29, 29, 11, 6, 11, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 11, 11, 11, 29, 29, 29, 50, 50, 45, 50, 50, 29, 29, 29, 6, 6, 6, 6, 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, 46]) total number of confs: 137 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435683763 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435683763 Building ZINC001435717976 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435717976 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/462 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/462' -> `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(COc2ccccc2)cc1) `ZINC001435717976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435717976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001435717976 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(COc2ccccc2)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.3', 'O.3', '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'] 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, 5, 12, 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, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 4, 7, 7, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 4, 32, 32, 32, 32, 32, 32, 32, 6, 6, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 2, 6, 6, 32, 32, 32, 32, 32, 32, 32, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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/182395/xbh-8058088.34/working/building/ZINC001435717976 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/463 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/463' -> `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(COc2ccccc2)cc1) `ZINC001435717976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435717976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001435717976 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(COc2ccccc2)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.3', 'O.3', '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'] 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, 5, 12, 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, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 2, 2, 6, 6, 2, 4, 35, 35, 35, 35, 35, 35, 35, 6, 6, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 6, 6, 35, 35, 35, 35, 35, 35, 35, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435717976 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976 Building ZINC001435717976 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435717976 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 462) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(COc2ccccc2)cc1) `ZINC001435717976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435717976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001435717976 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(COc2ccccc2)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.3', 'O.3', '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'] 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, 5, 12, 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, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 4, 7, 7, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 4, 32, 32, 32, 32, 32, 32, 32, 6, 6, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 2, 6, 6, 32, 32, 32, 32, 32, 32, 32, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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/182395/xbh-8058088.34/working/building/ZINC001435717976 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 463) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(COc2ccccc2)cc1) `ZINC001435717976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435717976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001435717976 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(COc2ccccc2)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.3', 'O.3', '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'] 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, 5, 12, 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, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 2, 2, 6, 6, 2, 4, 35, 35, 35, 35, 35, 35, 35, 6, 6, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 6, 6, 35, 35, 35, 35, 35, 35, 35, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435717976 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435717976 Building ZINC001435812464 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435812464 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/464 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/464' -> `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)Nc1sc2c(c1C(=O)c1ccc(C)cc1)CCCCC2) `ZINC001435812464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435812464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001435812464 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(C)cc1)CCCCC2 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', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 36, 36, 25, 36, 44, 44, 44, 44, 44, 44, 44, 44, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 44, 44, 44, 44, 44, 44, 44, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/465 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/465' -> `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)Nc1sc2c(c1C(=O)c1ccc(C)cc1)CCCCC2) `ZINC001435812464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435812464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001435812464 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(C)cc1)CCCCC2 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', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 36, 36, 24, 36, 44, 44, 44, 44, 44, 44, 44, 44, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 44, 44, 44, 44, 44, 44, 44, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36] 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435812464 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464 Building ZINC001435812464 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435812464 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 464) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(C)cc1)CCCCC2) `ZINC001435812464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435812464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001435812464 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(C)cc1)CCCCC2 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', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 36, 36, 25, 36, 44, 44, 44, 44, 44, 44, 44, 44, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 44, 44, 44, 44, 44, 44, 44, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 465) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(C)cc1)CCCCC2) `ZINC001435812464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435812464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001435812464 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(C)cc1)CCCCC2 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', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 36, 36, 24, 36, 44, 44, 44, 44, 44, 44, 44, 44, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 44, 44, 44, 44, 44, 44, 44, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36] 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435812464 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812464 Building ZINC001435812881 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435812881 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/466 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(OCc3ccccc3F)cc2)cc1Cl) `ZINC001435812881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435812881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435812881 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(OCc3ccccc3F)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 8, 8, 5, 5, 13, 13, 27, 27, 16, 27, 27, 27, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 8, 8, 13, 13, 27, 27, 27, 27, 8, 8, 2] 50 rigid atoms, others: [35, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/467 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/467' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(OCc3ccccc3F)cc2)cc1Cl) `ZINC001435812881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435812881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435812881 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(OCc3ccccc3F)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 8, 8, 7, 8, 14, 14, 26, 26, 14, 26, 26, 26, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 8, 8, 14, 14, 26, 26, 26, 26, 8, 8, 2] 50 rigid atoms, others: [35, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435812881 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881 Building ZINC001435812881 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435812881 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 466) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(OCc3ccccc3F)cc2)cc1Cl) `ZINC001435812881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435812881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435812881 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(OCc3ccccc3F)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 8, 8, 5, 5, 13, 13, 27, 27, 16, 27, 27, 27, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 8, 8, 13, 13, 27, 27, 27, 27, 8, 8, 2] 50 rigid atoms, others: [35, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 467) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(OCc3ccccc3F)cc2)cc1Cl) `ZINC001435812881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435812881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435812881 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(OCc3ccccc3F)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 8, 8, 7, 8, 14, 14, 26, 26, 14, 26, 26, 26, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 8, 8, 14, 14, 26, 26, 26, 26, 8, 8, 2] 50 rigid atoms, others: [35, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435812881 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435812881 Building ZINC001435817068 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435817068 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/468 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/468' -> `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)NCc1c(OC(C)C)ccc2ccccc21) `ZINC001435817068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435817068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001435817068 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1c(OC(C)C)ccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', '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'] 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, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 17, 17, 34, 41, 41, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 4, 11, 11, 41, 41, 41, 41, 41, 41, 41, 17, 17, 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/469 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/469' -> `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)NCc1c(OC(C)C)ccc2ccccc21) `ZINC001435817068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435817068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001435817068 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1c(OC(C)C)ccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', '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'] 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, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 17, 17, 34, 41, 41, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 4, 11, 11, 41, 41, 41, 41, 41, 41, 41, 17, 17, 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435817068 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068 Building ZINC001435817068 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435817068 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 468) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1c(OC(C)C)ccc2ccccc21) `ZINC001435817068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435817068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001435817068 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1c(OC(C)C)ccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', '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'] 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, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 17, 17, 34, 41, 41, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 4, 11, 11, 41, 41, 41, 41, 41, 41, 41, 17, 17, 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 469) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1c(OC(C)C)ccc2ccccc21) `ZINC001435817068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435817068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001435817068 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1c(OC(C)C)ccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', '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'] 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, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 17, 17, 34, 41, 41, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 4, 11, 11, 41, 41, 41, 41, 41, 41, 41, 17, 17, 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435817068 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817068 Building ZINC001435817113 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435817113 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/470 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Oc1ccc2ccccc2c1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435817113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435817113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001435817113 none CC(C)Oc1ccc2ccccc2c1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.2', 'C.2', 'Br', 'S.3', '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, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 36, 37, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 15, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 37, 37, 37, 37, 37, 37, 37, 21, 21, 21, 21, 21, 21, 15, 15, 5, 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]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/471 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/471' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Oc1ccc2ccccc2c1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435817113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435817113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001435817113 none CC(C)Oc1ccc2ccccc2c1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.2', 'C.2', 'Br', 'S.3', '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, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 36, 37, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 14, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 37, 37, 37, 37, 37, 37, 37, 20, 20, 20, 20, 20, 20, 14, 14, 4, 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]) total number of confs: 101 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435817113 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113 Building ZINC001435817113 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435817113 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 470) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)Oc1ccc2ccccc2c1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435817113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435817113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001435817113 none CC(C)Oc1ccc2ccccc2c1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.2', 'C.2', 'Br', 'S.3', '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, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 36, 37, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 15, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 37, 37, 37, 37, 37, 37, 37, 21, 21, 21, 21, 21, 21, 15, 15, 5, 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]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 471) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)Oc1ccc2ccccc2c1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435817113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435817113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001435817113 none CC(C)Oc1ccc2ccccc2c1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.2', 'C.2', 'Br', 'S.3', '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, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 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] 0 hydrogens 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, 36, 37, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 14, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 37, 37, 37, 37, 37, 37, 37, 20, 20, 20, 20, 20, 20, 14, 14, 4, 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]) total number of confs: 101 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435817113 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435817113 Building ZINC001435822320 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435822320 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/472 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cc2nnc3n2CCCCC3)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435822320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435822320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435822320 none O=C(Nc1ccc(Cc2nnc3n2CCCCC3)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.ar', 'C.ar', 'C.ar', 'Cl', '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'] 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, 1, 16, 1, 1, 16, 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, 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, 5, 5, 2, 4, 23, 24, 47, 47, 24, 47, 47, 47, 47, 47, 5, 5, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 5, 5, 23, 23, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 5, 5, 3, 1, 3] 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/473 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/473' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cc2nnc3n2CCCCC3)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435822320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435822320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435822320 none O=C(Nc1ccc(Cc2nnc3n2CCCCC3)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.ar', 'C.ar', 'C.ar', 'Cl', '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'] 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, 1, 16, 1, 1, 16, 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, 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, 5, 5, 2, 3, 24, 24, 47, 47, 24, 47, 47, 47, 47, 47, 5, 5, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 5, 5, 24, 24, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 5, 5, 3, 1, 3] 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435822320 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320 Building ZINC001435822320 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435822320 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 472) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1ccc(Cc2nnc3n2CCCCC3)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435822320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435822320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435822320 none O=C(Nc1ccc(Cc2nnc3n2CCCCC3)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.ar', 'C.ar', 'C.ar', 'Cl', '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'] 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, 1, 16, 1, 1, 16, 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, 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, 5, 5, 2, 4, 23, 24, 47, 47, 24, 47, 47, 47, 47, 47, 5, 5, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 5, 5, 23, 23, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 5, 5, 3, 1, 3] 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 473) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1ccc(Cc2nnc3n2CCCCC3)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435822320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435822320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435822320 none O=C(Nc1ccc(Cc2nnc3n2CCCCC3)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.ar', 'C.ar', 'C.ar', 'Cl', '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'] 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, 1, 16, 1, 1, 16, 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, 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, 5, 5, 2, 3, 24, 24, 47, 47, 24, 47, 47, 47, 47, 47, 5, 5, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 5, 5, 24, 24, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 5, 5, 3, 1, 3] 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435822320 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435822320 Building ZINC001435827830 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435827830 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/474 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nc3c(s2)C[C@@H](c2ccccc2)CC3)cc1Cl) `ZINC001435827830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435827830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435827830 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nc3c(s2)C[C@@H](c2ccccc2)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.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 14, 5, 5, 7, 1, 1, 1, 1, 1, 1, 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] 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] 0 hydrogens 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, 17, 26, 26, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 2, 2, 2, 4, 4, 4, 2, 2, 1, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 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: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/475 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/475' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2nc3c(s2)C[C@@H](c2ccccc2)CC3)cc1Cl) `ZINC001435827830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435827830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435827830 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2nc3c(s2)C[C@@H](c2ccccc2)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.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 14, 5, 5, 7, 1, 1, 1, 1, 1, 1, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 17, 27, 27, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 2, 2, 2, 2, 2, 1, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435827830 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830 Building ZINC001435827830 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435827830 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 474) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nc3c(s2)C[C@@H](c2ccccc2)CC3)cc1Cl) `ZINC001435827830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435827830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435827830 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nc3c(s2)C[C@@H](c2ccccc2)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.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 14, 5, 5, 7, 1, 1, 1, 1, 1, 1, 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] 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] 0 hydrogens 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, 17, 26, 26, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 2, 2, 2, 4, 4, 4, 2, 2, 1, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 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: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 475) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2nc3c(s2)C[C@@H](c2ccccc2)CC3)cc1Cl) `ZINC001435827830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435827830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435827830 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2nc3c(s2)C[C@@H](c2ccccc2)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.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 14, 5, 5, 7, 1, 1, 1, 1, 1, 1, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 17, 27, 27, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 2, 2, 2, 2, 2, 1, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435827830 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827830 Building ZINC001435827831 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435827831 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/476 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nc3c(s2)C[C@H](c2ccccc2)CC3)cc1Cl) `ZINC001435827831.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435827831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435827831 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nc3c(s2)C[C@H](c2ccccc2)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.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 14, 5, 5, 7, 1, 1, 1, 1, 1, 1, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 17, 27, 27, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 2, 2, 2, 2, 2, 1, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/477 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/477' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2nc3c(s2)C[C@H](c2ccccc2)CC3)cc1Cl) `ZINC001435827831.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435827831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435827831 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2nc3c(s2)C[C@H](c2ccccc2)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.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 14, 5, 5, 7, 1, 1, 1, 1, 1, 1, 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] 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] 0 hydrogens 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, 17, 27, 27, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 4, 4, 4, 2, 2, 1, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 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: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435827831 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831 Building ZINC001435827831 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435827831 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 476) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCc2nc3c(s2)C[C@H](c2ccccc2)CC3)cc1Cl) `ZINC001435827831.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435827831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435827831 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nc3c(s2)C[C@H](c2ccccc2)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.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 14, 5, 5, 7, 1, 1, 1, 1, 1, 1, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 17, 27, 27, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 2, 2, 2, 2, 2, 1, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 477) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCc2nc3c(s2)C[C@H](c2ccccc2)CC3)cc1Cl) `ZINC001435827831.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435827831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435827831 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2nc3c(s2)C[C@H](c2ccccc2)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.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 14, 5, 5, 7, 1, 1, 1, 1, 1, 1, 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] 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] 0 hydrogens 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, 17, 27, 27, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 4, 4, 4, 2, 2, 1, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 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: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435827831 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435827831 Building ZINC001435841496 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435841496 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/478 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1C1CCCC1) `ZINC001435841496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435841496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001435841496 none COC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1C1CCCC1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 5, 5, 5, 5, 5, 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] 0 hydrogens 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, 4, 17, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 4, 12, 24, 24, 24, 24, 17, 17, 17, 2, 3, 1, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/479 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/479' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1C1CCCC1) `ZINC001435841496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435841496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001435841496 none COC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1C1CCCC1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 5, 5, 5, 5, 5, 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] 0 hydrogens 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, 4, 16, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 4, 12, 20, 20, 20, 20, 16, 16, 16, 2, 3, 1, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435841496 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496 Building ZINC001435841496 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435841496 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 478) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1C1CCCC1) `ZINC001435841496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435841496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001435841496 none COC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1C1CCCC1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 5, 5, 5, 5, 5, 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] 0 hydrogens 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, 4, 17, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 4, 12, 24, 24, 24, 24, 17, 17, 17, 2, 3, 1, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 479) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1C1CCCC1) `ZINC001435841496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435841496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001435841496 none COC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1C1CCCC1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 5, 5, 5, 5, 5, 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] 0 hydrogens 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, 4, 16, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 4, 12, 20, 20, 20, 20, 16, 16, 16, 2, 3, 1, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435841496 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435841496 Building ZINC001435869672 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435869672 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/480 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCCCCCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001435869672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435869672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435869672 none CSCCCCCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', '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.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, 14, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 14, 14, 14, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 45, 46, 47, 48, 53, 54, 55] 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, 43, 44, 49, 50, 51, 52]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/481 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/481' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCCCCCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001435869672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435869672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435869672 none CSCCCCCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', '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.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, 14, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 14, 14, 14, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 45, 46, 47, 48, 53, 54, 55] 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, 43, 44, 49, 50, 51, 52]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435869672 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672 Building ZINC001435869672 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435869672 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 480) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCCCCCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001435869672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435869672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435869672 none CSCCCCCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', '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.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, 14, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 14, 14, 14, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 45, 46, 47, 48, 53, 54, 55] 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, 43, 44, 49, 50, 51, 52]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 481) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCCCCCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001435869672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435869672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435869672 none CSCCCCCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', '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.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, 14, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 14, 14, 14, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 45, 46, 47, 48, 53, 54, 55] 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, 43, 44, 49, 50, 51, 52]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435869672 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435869672 Building ZINC001435880246 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435880246 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/482 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c(Br)cc1Br) `ZINC001435880246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435880246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC001435880246 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c(Br)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'Br', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 17, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 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: [48, 35, 35, 35, 7, 7, 1, 7, 1, 1, 1, 5, 5, 2, 5, 5, 5, 35, 35, 35, 35, 35, 48, 48, 48, 35, 7, 5, 5, 5, 5, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/483 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/483' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c(Br)cc1Br) `ZINC001435880246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435880246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC001435880246 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c(Br)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'Br', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 17, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 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: [48, 35, 35, 35, 7, 7, 1, 7, 1, 1, 1, 5, 5, 1, 1, 5, 5, 35, 35, 35, 35, 35, 48, 48, 48, 35, 7, 5, 5, 5, 5, 35] 50 rigid atoms, others: [6, 8, 9, 10] 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435880246 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246 Building ZINC001435880246 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435880246 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 482) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c(Br)cc1Br) `ZINC001435880246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435880246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC001435880246 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c(Br)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'Br', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 17, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 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: [48, 35, 35, 35, 7, 7, 1, 7, 1, 1, 1, 5, 5, 2, 5, 5, 5, 35, 35, 35, 35, 35, 48, 48, 48, 35, 7, 5, 5, 5, 5, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 483) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c(Br)cc1Br) `ZINC001435880246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435880246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC001435880246 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c(Br)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'Br', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 17, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 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: [48, 35, 35, 35, 7, 7, 1, 7, 1, 1, 1, 5, 5, 1, 1, 5, 5, 35, 35, 35, 35, 35, 48, 48, 48, 35, 7, 5, 5, 5, 5, 35] 50 rigid atoms, others: [6, 8, 9, 10] 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435880246 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435880246 Building ZINC001435884918 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435884918 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/484 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccc(Cl)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1C) `ZINC001435884918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435884918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435884918 none Cc1nn(c2ccc(Cl)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', 'Cl', '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, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 25, 25, 25, 25, 25, 25, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 18, 18, 18, 18, 18, 25, 25, 25, 25, 5, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 18, 18, 18] 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: 58 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/485 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/485' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccc(Cl)cc2)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1C) `ZINC001435884918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435884918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435884918 none Cc1nn(c2ccc(Cl)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', 'Cl', '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, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 25, 27, 27, 27, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 19, 19, 19, 19, 19, 27, 27, 27, 27, 5, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 19, 19, 19] 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: 81 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435884918 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918 Building ZINC001435884918 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435884918 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 484) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2ccc(Cl)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1C) `ZINC001435884918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435884918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435884918 none Cc1nn(c2ccc(Cl)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', 'Cl', '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, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 25, 25, 25, 25, 25, 25, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 18, 18, 18, 18, 18, 25, 25, 25, 25, 5, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 18, 18, 18] 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: 58 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 485) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2ccc(Cl)cc2)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1C) `ZINC001435884918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435884918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435884918 none Cc1nn(c2ccc(Cl)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', 'Cl', '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, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 25, 27, 27, 27, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 19, 19, 19, 19, 19, 27, 27, 27, 27, 5, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 19, 19, 19] 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: 81 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435884918 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435884918 Building ZINC001435887381 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435887381 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/486 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(F)cc1) `ZINC001435887381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435887381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435887381 none CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', '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', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 4, 4, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 10, 10, 2, 4, 4, 4, 6, 6, 6, 6, 6, 4, 4, 4, 5, 9, 9, 9, 9] 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, 54, 55, 56]) total number of confs: 98 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/487 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/487' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(F)cc1) `ZINC001435887381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435887381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435887381 none CCCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', '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', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 10, 10, 2, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 5, 9, 9, 9, 9] 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, 54, 55, 56]) total number of confs: 99 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435887381 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381 Building ZINC001435887381 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435887381 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 486) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(F)cc1) `ZINC001435887381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435887381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435887381 none CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', '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', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 4, 4, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 10, 10, 2, 4, 4, 4, 6, 6, 6, 6, 6, 4, 4, 4, 5, 9, 9, 9, 9] 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, 54, 55, 56]) total number of confs: 98 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 487) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(F)cc1) `ZINC001435887381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435887381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435887381 none CCCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', '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', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 10, 10, 2, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 5, 9, 9, 9, 9] 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, 54, 55, 56]) total number of confs: 99 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435887381 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435887381 Building ZINC001435891054 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435891054 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/488 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)C[C@@H](C)Oc2ccc(Cl)c(Cl)c2)cc1Cl) `ZINC001435891054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435891054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001435891054 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)C[C@@H](C)Oc2ccc(Cl)c(Cl)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', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 16, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 9, 10, 10, 10, 16, 27, 27, 20, 27, 27, 27, 27, 2, 2, 2, 5, 5, 5, 2, 2, 5, 5, 5, 9, 9, 10, 10, 10, 27, 27, 27, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/489 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/489' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)C[C@@H](C)Oc2ccc(Cl)c(Cl)c2)cc1Cl) `ZINC001435891054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435891054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001435891054 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)C[C@@H](C)Oc2ccc(Cl)c(Cl)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', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 16, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 7, 9, 9, 9, 14, 27, 27, 23, 27, 27, 27, 27, 3, 3, 3, 5, 5, 5, 3, 3, 3, 3, 3, 7, 7, 9, 9, 9, 27, 27, 27, 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]) total number of confs: 100 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435891054 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054 Building ZINC001435891054 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435891054 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 488) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)C[C@@H](C)Oc2ccc(Cl)c(Cl)c2)cc1Cl) `ZINC001435891054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435891054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001435891054 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)C[C@@H](C)Oc2ccc(Cl)c(Cl)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', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 16, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 9, 10, 10, 10, 16, 27, 27, 20, 27, 27, 27, 27, 2, 2, 2, 5, 5, 5, 2, 2, 5, 5, 5, 9, 9, 10, 10, 10, 27, 27, 27, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 489) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)C[C@@H](C)Oc2ccc(Cl)c(Cl)c2)cc1Cl) `ZINC001435891054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435891054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001435891054 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)C[C@@H](C)Oc2ccc(Cl)c(Cl)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', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 16, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 7, 9, 9, 9, 14, 27, 27, 23, 27, 27, 27, 27, 3, 3, 3, 5, 5, 5, 3, 3, 3, 3, 3, 7, 7, 9, 9, 9, 27, 27, 27, 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]) total number of confs: 100 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435891054 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891054 Building ZINC001435891056 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435891056 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/490 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)C[C@H](C)Oc2ccc(Cl)c(Cl)c2)cc1Cl) `ZINC001435891056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435891056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001435891056 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)C[C@H](C)Oc2ccc(Cl)c(Cl)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', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 16, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 8, 8, 8, 13, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 6, 6, 6, 3, 3, 3, 3, 3, 6, 6, 8, 8, 8, 26, 26, 26, 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]) total number of confs: 79 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/491 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/491' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)C[C@H](C)Oc2ccc(Cl)c(Cl)c2)cc1Cl) `ZINC001435891056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435891056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001435891056 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)C[C@H](C)Oc2ccc(Cl)c(Cl)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', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 16, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 9, 11, 11, 11, 17, 28, 28, 21, 28, 28, 28, 28, 2, 2, 2, 5, 5, 5, 2, 2, 5, 5, 5, 9, 9, 11, 11, 11, 28, 28, 28, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435891056 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056 Building ZINC001435891056 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435891056 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 490) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)C[C@H](C)Oc2ccc(Cl)c(Cl)c2)cc1Cl) `ZINC001435891056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435891056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001435891056 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)C[C@H](C)Oc2ccc(Cl)c(Cl)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', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 16, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 8, 8, 8, 13, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 6, 6, 6, 3, 3, 3, 3, 3, 6, 6, 8, 8, 8, 26, 26, 26, 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]) total number of confs: 79 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 491) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)C[C@H](C)Oc2ccc(Cl)c(Cl)c2)cc1Cl) `ZINC001435891056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435891056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001435891056 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)C[C@H](C)Oc2ccc(Cl)c(Cl)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', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 16, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 9, 11, 11, 11, 17, 28, 28, 21, 28, 28, 28, 28, 2, 2, 2, 5, 5, 5, 2, 2, 5, 5, 5, 9, 9, 11, 11, 11, 28, 28, 28, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435891056 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435891056 Building ZINC001435907059 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435907059 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/492 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/492' -> `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)Nc1cccc2ccn(C)c21) `ZINC001435907059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435907059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435907059 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc2ccn(C)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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'] dock atom 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, 8, 5, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 10, 10, 3, 10, 3, 3, 3, 6, 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]) total number of confs: 47 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/493 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/493' -> `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)Nc1cccc2ccn(C)c21) `ZINC001435907059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435907059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435907059 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc2ccn(C)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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'] dock atom 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, 8, 5, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 6, 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]) total number of confs: 51 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435907059 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059 Building ZINC001435907059 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435907059 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 492) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc2ccn(C)c21) `ZINC001435907059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435907059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435907059 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc2ccn(C)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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'] dock atom 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, 8, 5, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 10, 10, 3, 10, 3, 3, 3, 6, 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]) total number of confs: 47 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 493) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc2ccn(C)c21) `ZINC001435907059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435907059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435907059 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc2ccn(C)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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'] dock atom 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, 8, 5, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 6, 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]) total number of confs: 51 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435907059 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907059 Building ZINC001435907131 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435907131 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/494 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2C1) `ZINC001435907131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435907131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435907131 none CC(C)(C)OC(=O)N1Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens 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, 27, 50, 27, 27, 27, 27, 27, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 8, 8, 2, 2, 1, 2, 27, 27, 27] 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: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/495 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/495' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2C1) `ZINC001435907131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435907131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435907131 none CC(C)(C)OC(=O)N1Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens 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, 27, 50, 27, 27, 27, 27, 27, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 8, 8, 2, 2, 1, 2, 27, 27, 27] 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: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435907131 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131 Building ZINC001435907131 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435907131 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 494) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)OC(=O)N1Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2C1) `ZINC001435907131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435907131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435907131 none CC(C)(C)OC(=O)N1Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens 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, 27, 50, 27, 27, 27, 27, 27, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 8, 8, 2, 2, 1, 2, 27, 27, 27] 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: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 495) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)OC(=O)N1Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2C1) `ZINC001435907131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435907131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001435907131 none CC(C)(C)OC(=O)N1Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens 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, 27, 50, 27, 27, 27, 27, 27, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 8, 8, 2, 2, 1, 2, 27, 27, 27] 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: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435907131 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435907131 Building ZINC001435910447 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435910447 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/496 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2cc3ccccc3o2)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435910447.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435910447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001435910447 none O=C(Nc1nnc(c2cc3ccccc3o2)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 34, 34, 34, 34, 34, 34, 34, 34, 9, 1, 1, 1, 11, 11, 11, 11, 11, 5, 34, 34, 34, 34, 34, 11, 11] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/497 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/497' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2cc3ccccc3o2)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435910447.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435910447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001435910447 none O=C(Nc1nnc(c2cc3ccccc3o2)s1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 37, 37, 37, 37, 37, 37, 37, 37, 9, 1, 1, 1, 11, 11, 11, 11, 11, 5, 37, 37, 37, 37, 37, 11, 11] 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435910447 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447 Building ZINC001435910447 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435910447 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 496) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1nnc(c2cc3ccccc3o2)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435910447.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435910447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001435910447 none O=C(Nc1nnc(c2cc3ccccc3o2)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 34, 34, 34, 34, 34, 34, 34, 34, 9, 1, 1, 1, 11, 11, 11, 11, 11, 5, 34, 34, 34, 34, 34, 11, 11] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 497) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1nnc(c2cc3ccccc3o2)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435910447.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435910447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001435910447 none O=C(Nc1nnc(c2cc3ccccc3o2)s1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 37, 37, 37, 37, 37, 37, 37, 37, 9, 1, 1, 1, 11, 11, 11, 11, 11, 5, 37, 37, 37, 37, 37, 11, 11] 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435910447 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435910447 Building ZINC001435940075 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435940075 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/498 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3Br)CC2)cc1Cl) `ZINC001435940075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435940075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001435940075 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3Br)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.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 5, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 5, 9, 11, 11, 11, 11, 24, 24, 11, 24, 24, 24, 11, 11, 6, 6, 6, 8, 8, 8, 6, 6, 11, 11, 11, 11, 11, 24, 24, 11, 24, 11, 11, 11, 11, 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, 40, 41, 42, 43, 44]) total number of confs: 79 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/499 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/499' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3Br)CC2)cc1Cl) `ZINC001435940075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435940075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001435940075 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3Br)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.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 5, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 4, 9, 13, 13, 13, 13, 24, 24, 13, 24, 24, 24, 13, 13, 6, 6, 6, 9, 9, 9, 6, 6, 13, 13, 13, 13, 13, 24, 24, 13, 24, 13, 13, 13, 13, 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, 40, 41, 42, 43, 44]) total number of confs: 91 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435940075 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075 Building ZINC001435940075 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435940075 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 498) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3Br)CC2)cc1Cl) `ZINC001435940075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435940075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001435940075 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3Br)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.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 5, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 5, 9, 11, 11, 11, 11, 24, 24, 11, 24, 24, 24, 11, 11, 6, 6, 6, 8, 8, 8, 6, 6, 11, 11, 11, 11, 11, 24, 24, 11, 24, 11, 11, 11, 11, 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, 40, 41, 42, 43, 44]) total number of confs: 79 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 499) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3Br)CC2)cc1Cl) `ZINC001435940075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435940075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001435940075 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3Br)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.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 5, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 4, 9, 13, 13, 13, 13, 24, 24, 13, 24, 24, 24, 13, 13, 6, 6, 6, 9, 9, 9, 6, 6, 13, 13, 13, 13, 13, 24, 24, 13, 24, 13, 13, 13, 13, 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, 40, 41, 42, 43, 44]) total number of confs: 91 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435940075 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435940075 Building ZINC001435948572 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435948572 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/500 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@@H]2C) `ZINC001435948572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435948572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435948572 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@@H]2C 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', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 13, 14, 40, 40, 49, 49, 49, 49, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 4, 49, 49, 49, 49, 49, 49, 49, 49, 49, 14, 14, 14, 14, 14, 14, 14, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/501 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/501' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@@H]2C) `ZINC001435948572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435948572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435948572 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@@H]2C 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', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 3, 3, 12, 12, 12, 12, 12, 38, 38, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 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, 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: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435948572 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572 Building ZINC001435948572 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435948572 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 500) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@@H]2C) `ZINC001435948572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435948572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435948572 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@@H]2C 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', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 13, 14, 40, 40, 49, 49, 49, 49, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 4, 49, 49, 49, 49, 49, 49, 49, 49, 49, 14, 14, 14, 14, 14, 14, 14, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 501) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@@H]2C) `ZINC001435948572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435948572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435948572 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@@H]2C 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', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 3, 3, 12, 12, 12, 12, 12, 38, 38, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 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, 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: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435948572 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948572 Building ZINC001435948574 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435948574 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/502 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@H]2C) `ZINC001435948574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435948574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435948574 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@H]2C 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', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 9, 11, 9, 9, 9, 34, 34, 45, 45, 45, 45, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 4, 45, 45, 45, 46, 45, 45, 45, 45, 45, 11, 11, 11, 11, 11, 11, 11, 11] 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: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/503 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/503' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@H]2C) `ZINC001435948574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435948574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435948574 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@H]2C 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', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 9, 12, 9, 9, 9, 37, 37, 46, 46, 46, 46, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 4, 46, 46, 46, 48, 47, 46, 46, 46, 46, 12, 12, 12, 12, 12, 12, 12, 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, 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: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435948574 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574 Building ZINC001435948574 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435948574 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 502) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@H]2C) `ZINC001435948574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435948574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435948574 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@H]2C 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', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 9, 11, 9, 9, 9, 34, 34, 45, 45, 45, 45, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 4, 45, 45, 45, 46, 45, 45, 45, 45, 45, 11, 11, 11, 11, 11, 11, 11, 11] 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: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 503) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@H]2C) `ZINC001435948574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435948574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435948574 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@@H](C)O[C@H]2C 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', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 9, 12, 9, 9, 9, 37, 37, 46, 46, 46, 46, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 4, 46, 46, 46, 48, 47, 46, 46, 46, 46, 12, 12, 12, 12, 12, 12, 12, 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, 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: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435948574 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948574 Building ZINC001435948575 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435948575 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/504 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@@H]2C) `ZINC001435948575.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435948575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435948575 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@@H]2C 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', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 8, 11, 8, 8, 8, 35, 38, 48, 48, 48, 48, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 11, 11, 11, 11, 11, 11, 11, 11] 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/182395/xbh-8058088.34/working/building/ZINC001435948575 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/505 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/505' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@@H]2C) `ZINC001435948575.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435948575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435948575 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@@H]2C 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', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 9, 11, 9, 9, 9, 35, 36, 46, 46, 46, 46, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 4, 46, 46, 46, 46, 46, 46, 46, 46, 46, 11, 11, 11, 11, 11, 11, 11, 11] 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: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435948575 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575 Building ZINC001435948575 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435948575 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 504) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@@H]2C) `ZINC001435948575.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435948575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435948575 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@@H]2C 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', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 8, 11, 8, 8, 8, 35, 38, 48, 48, 48, 48, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 11, 11, 11, 11, 11, 11, 11, 11] 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/182395/xbh-8058088.34/working/building/ZINC001435948575 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 505) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@@H]2C) `ZINC001435948575.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435948575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435948575 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@@H]2C 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', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 9, 11, 9, 9, 9, 35, 36, 46, 46, 46, 46, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 4, 46, 46, 46, 46, 46, 46, 46, 46, 46, 11, 11, 11, 11, 11, 11, 11, 11] 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: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435948575 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948575 Building ZINC001435948576 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435948576 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/506 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@H]2C) `ZINC001435948576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435948576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435948576 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@H]2C 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', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 3, 3, 11, 11, 11, 11, 11, 37, 37, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11] 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: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/507 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/507' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@H]2C) `ZINC001435948576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435948576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435948576 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@H]2C 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', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 14, 14, 14, 13, 14, 41, 41, 49, 49, 49, 49, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 4, 49, 49, 49, 49, 49, 49, 49, 49, 49, 14, 14, 14, 14, 14, 14, 14, 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, 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/182395/xbh-8058088.34/working/building/ZINC001435948576 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435948576 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576 Building ZINC001435948576 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435948576 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 506) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@H]2C) `ZINC001435948576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435948576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435948576 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@H]2C 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', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 3, 3, 11, 11, 11, 11, 11, 37, 37, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11] 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: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 507) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@H]2C) `ZINC001435948576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435948576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001435948576 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)OC(C)(C)C)C[C@H](C)O[C@H]2C 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', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 5, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 14, 14, 14, 13, 14, 41, 41, 49, 49, 49, 49, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 4, 49, 49, 49, 49, 49, 49, 49, 49, 49, 14, 14, 14, 14, 14, 14, 14, 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, 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/182395/xbh-8058088.34/working/building/ZINC001435948576 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435948576 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435948576 Building ZINC001435982246 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435982246 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/508 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CC(F)(F)F)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001435982246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435982246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001435982246 none O=C(N[C@H](CC(F)(F)F)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 15, 15, 15, 1, 1, 1, 1, 17, 1, 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] 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] 0 hydrogens 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, 9, 9, 15, 15, 15, 15, 9, 15, 15, 11, 9, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 15, 15, 15, 15, 15, 15, 6, 6, 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]) total number of confs: 100 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/509 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/509' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CC(F)(F)F)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001435982246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435982246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001435982246 none O=C(N[C@H](CC(F)(F)F)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 15, 15, 15, 1, 1, 1, 1, 17, 1, 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] 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] 0 hydrogens 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, 8, 8, 13, 13, 13, 13, 8, 14, 14, 8, 8, 14, 14, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 13, 13, 14, 14, 14, 14, 6, 6, 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]) total number of confs: 99 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435982246 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246 Building ZINC001435982246 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435982246 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 508) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@H](CC(F)(F)F)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001435982246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435982246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001435982246 none O=C(N[C@H](CC(F)(F)F)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 15, 15, 15, 1, 1, 1, 1, 17, 1, 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] 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] 0 hydrogens 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, 9, 9, 15, 15, 15, 15, 9, 15, 15, 11, 9, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 15, 15, 15, 15, 15, 15, 6, 6, 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]) total number of confs: 100 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 509) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@H](CC(F)(F)F)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001435982246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435982246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001435982246 none O=C(N[C@H](CC(F)(F)F)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 15, 15, 15, 1, 1, 1, 1, 17, 1, 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] 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] 0 hydrogens 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, 8, 8, 13, 13, 13, 13, 8, 14, 14, 8, 8, 14, 14, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 13, 13, 14, 14, 14, 14, 6, 6, 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]) total number of confs: 99 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001435982246 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001435982246 Building ZINC001436000261 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436000261 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/510 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCCCCCc2nc(c3ccc(Cl)cc3)no2)c1) `ZINC001436000261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436000261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436000261 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCCCCCc2nc(c3ccc(Cl)cc3)no2)c1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.3', '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', '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, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 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] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 2, 2, 2, 2, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 27, 27, 27, 27, 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, 51, 52, 53]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/511 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/511' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCCCCCc2nc(c3ccc(Cl)cc3)no2)c1) `ZINC001436000261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436000261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436000261 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCCCCCc2nc(c3ccc(Cl)cc3)no2)c1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.3', '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', '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, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 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] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 2, 2, 2, 2, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 27, 27, 27, 27, 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, 51, 52, 53]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436000261 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261 Building ZINC001436000261 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436000261 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 510) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCCCCCc2nc(c3ccc(Cl)cc3)no2)c1) `ZINC001436000261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436000261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436000261 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCCCCCc2nc(c3ccc(Cl)cc3)no2)c1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.3', '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', '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, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 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] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 2, 2, 2, 2, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 27, 27, 27, 27, 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, 51, 52, 53]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 511) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCCCCCc2nc(c3ccc(Cl)cc3)no2)c1) `ZINC001436000261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436000261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436000261 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCCCCCc2nc(c3ccc(Cl)cc3)no2)c1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.3', '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', '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, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 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] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 2, 2, 2, 2, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 27, 27, 27, 27, 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, 51, 52, 53]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436000261 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436000261 Building ZINC001436011293 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436011293 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/512 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)cc1OCCC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436011293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436011293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001436011293 none O=C(Nc1ccc(F)cc1OCCC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 12, 5, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 24, 41, 44, 44, 44, 44, 1, 1, 1, 6, 6, 6, 6, 6, 3, 6, 6, 6, 41, 41, 44, 44, 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]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/513 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/513' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)cc1OCCC(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436011293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436011293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001436011293 none O=C(Nc1ccc(F)cc1OCCC(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 12, 5, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 22, 40, 43, 43, 43, 43, 1, 1, 1, 6, 6, 6, 6, 6, 3, 6, 6, 6, 40, 40, 43, 43, 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436011293 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293 Building ZINC001436011293 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436011293 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 512) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(F)cc1OCCC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436011293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436011293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001436011293 none O=C(Nc1ccc(F)cc1OCCC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 12, 5, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 24, 41, 44, 44, 44, 44, 1, 1, 1, 6, 6, 6, 6, 6, 3, 6, 6, 6, 41, 41, 44, 44, 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]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 513) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/513: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(F)cc1OCCC(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436011293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436011293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001436011293 none O=C(Nc1ccc(F)cc1OCCC(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 12, 5, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 22, 40, 43, 43, 43, 43, 1, 1, 1, 6, 6, 6, 6, 6, 3, 6, 6, 6, 40, 40, 43, 43, 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436011293 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436011293 Building ZINC001436031171 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436031171 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/514 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/514' -> `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(F)(F)CC1) `ZINC001436031171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436031171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436031171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1CCC(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.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', 'F', 'F', 'C.3', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 9, 9, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/515 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/515' -> `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(F)(F)CC1) `ZINC001436031171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436031171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436031171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1CCC(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.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', 'F', 'F', 'C.3', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436031171 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171 Building ZINC001436031171 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436031171 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 514) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1CCC(F)(F)CC1) `ZINC001436031171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436031171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436031171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1CCC(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.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', 'F', 'F', 'C.3', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 9, 9, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 515) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1CCC(F)(F)CC1) `ZINC001436031171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436031171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436031171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1CCC(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.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', 'F', 'F', 'C.3', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436031171 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436031171 Building ZINC001436061583 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436061583 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/516 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(Br)cc1)CCC2) `ZINC001436061583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436061583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001436061583 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(Br)cc1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', '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', 'Br', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 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, 9, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 6, 6, 6, 29, 29, 29, 29, 29, 49, 49, 50, 50, 49, 50, 50, 50, 29, 29, 29, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 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]) total number of confs: 123 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/517 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/517' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(Br)cc1)CCC2) `ZINC001436061583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436061583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001436061583 none CC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(Br)cc1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', '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', 'Br', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 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, 9, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 6, 30, 30, 30, 30, 30, 48, 48, 49, 49, 49, 49, 49, 49, 30, 30, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 49, 49, 49, 49, 30, 30, 30, 30, 30, 30] 49 rigid atoms, others: [1, 4, 5, 6] set([0, 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]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436061583 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583 Building ZINC001436061583 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436061583 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 516) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(Br)cc1)CCC2) `ZINC001436061583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436061583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001436061583 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(Br)cc1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', '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', 'Br', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 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, 9, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 6, 6, 6, 29, 29, 29, 29, 29, 49, 49, 50, 50, 49, 50, 50, 50, 29, 29, 29, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 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]) total number of confs: 123 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 517) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(Br)cc1)CCC2) `ZINC001436061583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436061583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001436061583 none CC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(Br)cc1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', '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', 'Br', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 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, 9, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 6, 30, 30, 30, 30, 30, 48, 48, 49, 49, 49, 49, 49, 49, 30, 30, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 49, 49, 49, 49, 30, 30, 30, 30, 30, 30] 49 rigid atoms, others: [1, 4, 5, 6] set([0, 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]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436061583 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436061583 Building ZINC001436079165 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436079165 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/518 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/518' -> `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)Cc1cc(C)ccc1F) `ZINC001436079165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436079165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436079165 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1cc(C)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 7, 10, 10, 10, 7, 10, 10, 10, 3, 3, 3, 10, 10, 3, 10, 3, 3, 3, 5, 5, 5, 7, 7, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/519 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/519' -> `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)Cc1cc(C)ccc1F) `ZINC001436079165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436079165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436079165 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1cc(C)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 7, 9, 9, 9, 7, 9, 9, 9, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 5, 5, 5, 7, 7, 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436079165 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165 Building ZINC001436079165 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436079165 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 518) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1cc(C)ccc1F) `ZINC001436079165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436079165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436079165 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1cc(C)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 7, 10, 10, 10, 7, 10, 10, 10, 3, 3, 3, 10, 10, 3, 10, 3, 3, 3, 5, 5, 5, 7, 7, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 519) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1cc(C)ccc1F) `ZINC001436079165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436079165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436079165 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1cc(C)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 7, 9, 9, 9, 7, 9, 9, 9, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 5, 5, 5, 7, 7, 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436079165 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436079165 Building ZINC001436091956 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436091956 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/520 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/520' -> `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)Nc1ccccc1CN(C)c1ccccc1) `ZINC001436091956.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436091956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001436091956 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)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.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.3', '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', '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, 5, 8, 5, 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, 7] dock 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, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 7, 3, 7, 7, 7, 21, 43, 43, 43, 43, 43, 43, 43, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 7, 7, 3, 7, 21, 21, 43, 43, 43, 43, 43, 43, 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, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/521 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/521' -> `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)Nc1ccccc1CN(C)c1ccccc1) `ZINC001436091956.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436091956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001436091956 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)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.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.3', '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', '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, 5, 8, 5, 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, 7] dock 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, 3, 3, 3, 8, 8, 3, 8, 8, 8, 23, 43, 43, 43, 43, 43, 43, 43, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 8, 8, 5, 8, 23, 23, 43, 43, 43, 43, 43, 43, 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, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436091956 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956 Building ZINC001436091956 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436091956 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 520) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)c1ccccc1) `ZINC001436091956.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436091956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001436091956 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)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.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.3', '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', '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, 5, 8, 5, 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, 7] dock 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, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 7, 3, 7, 7, 7, 21, 43, 43, 43, 43, 43, 43, 43, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 7, 7, 3, 7, 21, 21, 43, 43, 43, 43, 43, 43, 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, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 521) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)c1ccccc1) `ZINC001436091956.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436091956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001436091956 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)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.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.3', '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', '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, 5, 8, 5, 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, 7] dock 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, 3, 3, 3, 8, 8, 3, 8, 8, 8, 23, 43, 43, 43, 43, 43, 43, 43, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 8, 8, 5, 8, 23, 23, 43, 43, 43, 43, 43, 43, 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, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436091956 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436091956 Building ZINC001436093828 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436093828 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/522 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(c2ccc(Br)o2)ncn1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436093828.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436093828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC001436093828 none O=C(Nc1cc(c2ccc(Br)o2)ncn1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'O.3', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 12, 8, 1, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 46, 46, 46, 46, 46, 8, 8, 8, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 4, 8, 46, 46, 8, 4, 2, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/523 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/523' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(c2ccc(Br)o2)ncn1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436093828.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436093828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC001436093828 none O=C(Nc1cc(c2ccc(Br)o2)ncn1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'O.3', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 12, 8, 1, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 46, 46, 46, 46, 46, 8, 8, 8, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 4, 8, 46, 46, 8, 4, 1, 4] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436093828 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828 Building ZINC001436093828 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436093828 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 522) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cc(c2ccc(Br)o2)ncn1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436093828.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436093828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC001436093828 none O=C(Nc1cc(c2ccc(Br)o2)ncn1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'O.3', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 12, 8, 1, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 46, 46, 46, 46, 46, 8, 8, 8, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 4, 8, 46, 46, 8, 4, 2, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 523) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cc(c2ccc(Br)o2)ncn1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436093828.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436093828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC001436093828 none O=C(Nc1cc(c2ccc(Br)o2)ncn1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'O.3', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 12, 8, 1, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 46, 46, 46, 46, 46, 8, 8, 8, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 4, 8, 46, 46, 8, 4, 1, 4] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436093828 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436093828 Building ZINC001436128651 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436128651 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/524 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(Br)c1) `ZINC001436128651.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436128651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001436128651 none CCCC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 6, 23, 23, 18, 23, 23, 23, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 23, 23, 23, 23] 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/525 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/525' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(Br)c1) `ZINC001436128651.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436128651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001436128651 none CCCC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 6, 22, 22, 22, 22, 22, 22, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 22, 22, 22, 22] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436128651 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651 Building ZINC001436128651 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436128651 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 524) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(Br)c1) `ZINC001436128651.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436128651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001436128651 none CCCC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 6, 23, 23, 18, 23, 23, 23, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 23, 23, 23, 23] 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 525) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(Br)c1) `ZINC001436128651.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436128651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001436128651 none CCCC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 6, 22, 22, 22, 22, 22, 22, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 22, 22, 22, 22] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436128651 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128651 Building ZINC001436128653 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436128653 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/526 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(Br)c1) `ZINC001436128653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436128653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001436128653 none CCCC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 6, 23, 23, 16, 23, 23, 23, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 23, 23, 22, 23] 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]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/527 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/527' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(Br)c1) `ZINC001436128653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436128653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001436128653 none CCCC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 6, 24, 24, 16, 24, 24, 24, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 24, 24, 16, 24] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436128653 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653 Building ZINC001436128653 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436128653 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 526) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(Br)c1) `ZINC001436128653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436128653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001436128653 none CCCC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 6, 23, 23, 16, 23, 23, 23, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 23, 23, 22, 23] 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]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 527) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(Br)c1) `ZINC001436128653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436128653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001436128653 none CCCC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 6, 24, 24, 16, 24, 24, 24, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 24, 24, 16, 24] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436128653 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436128653 Building ZINC001436156557 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436156557 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/528 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCCCC2)c2ncccc12)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436156557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436156557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436156557 none O=C(Nc1ccc(N2CCCCC2)c2ncccc12)[C@@]([O-])([SiH3])c1ccc(Br)s1 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.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 11, 11, 11, 16, 39, 39, 39, 39, 39, 11, 11, 11, 11, 11, 11, 1, 1, 1, 8, 8, 8, 8, 8, 4, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 11, 11, 11, 8, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/529 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCCCC2)c2ncccc12)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436156557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436156557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436156557 none O=C(Nc1ccc(N2CCCCC2)c2ncccc12)[C@]([O-])([SiH3])c1ccc(Br)s1 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.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 11, 11, 11, 16, 39, 39, 39, 39, 39, 11, 11, 11, 11, 11, 11, 1, 1, 1, 8, 8, 8, 8, 8, 4, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 11, 11, 11, 8, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436156557 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557 Building ZINC001436156557 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436156557 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 528) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1ccc(N2CCCCC2)c2ncccc12)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436156557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436156557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436156557 none O=C(Nc1ccc(N2CCCCC2)c2ncccc12)[C@@]([O-])([SiH3])c1ccc(Br)s1 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.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 11, 11, 11, 16, 39, 39, 39, 39, 39, 11, 11, 11, 11, 11, 11, 1, 1, 1, 8, 8, 8, 8, 8, 4, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 11, 11, 11, 8, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 529) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1ccc(N2CCCCC2)c2ncccc12)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436156557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436156557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436156557 none O=C(Nc1ccc(N2CCCCC2)c2ncccc12)[C@]([O-])([SiH3])c1ccc(Br)s1 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.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 11, 11, 11, 16, 39, 39, 39, 39, 39, 11, 11, 11, 11, 11, 11, 1, 1, 1, 8, 8, 8, 8, 8, 4, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 11, 11, 11, 8, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436156557 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436156557 Building ZINC001436159752 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436159752 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/530 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cccc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)n2)c1) `ZINC001436159752.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436159752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436159752 none CCOc1cccc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.2', 'C.2', 'Br', 'S.3', 'N.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 35, 47, 47, 47, 47, 47, 35, 35, 35, 4, 4, 4, 2, 4, 4, 35] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/531 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/531' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cccc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)n2)c1) `ZINC001436159752.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436159752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436159752 none CCOc1cccc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.2', 'C.2', 'Br', 'S.3', 'N.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 35, 47, 47, 47, 47, 47, 35, 35, 35, 4, 4, 4, 2, 4, 4, 35] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436159752 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752 Building ZINC001436159752 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436159752 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 530) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCOc1cccc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)n2)c1) `ZINC001436159752.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436159752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436159752 none CCOc1cccc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.2', 'C.2', 'Br', 'S.3', 'N.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 35, 47, 47, 47, 47, 47, 35, 35, 35, 4, 4, 4, 2, 4, 4, 35] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 531) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCOc1cccc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)n2)c1) `ZINC001436159752.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436159752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436159752 none CCOc1cccc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.2', 'C.2', 'Br', 'S.3', 'N.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 35, 47, 47, 47, 47, 47, 35, 35, 35, 4, 4, 4, 2, 4, 4, 35] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436159752 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436159752 Building ZINC001436181945 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436181945 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/532 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(I)cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001436181945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436181945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001436181945 none Cc1cc(I)cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 18, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 19, 33, 33, 33, 6, 6, 1, 6, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 33, 33, 33, 33, 20, 33, 6, 6, 1, 6, 33] 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/533 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/533' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(I)cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001436181945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436181945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001436181945 none Cc1cc(I)cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 18, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 16, 32, 32, 32, 6, 6, 1, 6, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 32, 32, 32, 32, 20, 32, 6, 6, 1, 6, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436181945 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945 Building ZINC001436181945 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436181945 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 532) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(I)cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001436181945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436181945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001436181945 none Cc1cc(I)cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 18, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 19, 33, 33, 33, 6, 6, 1, 6, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 33, 33, 33, 33, 20, 33, 6, 6, 1, 6, 33] 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 533) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(I)cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001436181945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436181945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001436181945 none Cc1cc(I)cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 18, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 16, 32, 32, 32, 6, 6, 1, 6, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 32, 32, 32, 32, 20, 32, 6, 6, 1, 6, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436181945 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436181945 Building ZINC001436200817 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436200817 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/534 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC)c(CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)C)c1) `ZINC001436200817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436200817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001436200817 none COc1ccc(OC)c(CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 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] dock color type numbers: [7, 3, 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] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 19, 9, 6, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 6, 11, 11, 11, 12, 20, 20, 20, 12, 12, 19, 19, 19, 9, 9, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 105 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/535 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/535' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC)c(CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)C)c1) `ZINC001436200817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436200817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001436200817 none COc1ccc(OC)c(CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 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] dock color type numbers: [7, 3, 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] 0 hydrogens 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, 13, 13, 13, 20, 10, 6, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 6, 11, 11, 11, 13, 21, 21, 21, 13, 13, 20, 20, 20, 10, 10, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 106 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436200817 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817 Building ZINC001436200817 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436200817 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 534) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc(OC)c(CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)C)c1) `ZINC001436200817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436200817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001436200817 none COc1ccc(OC)c(CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 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] dock color type numbers: [7, 3, 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] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 19, 9, 6, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 6, 11, 11, 11, 12, 20, 20, 20, 12, 12, 19, 19, 19, 9, 9, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 105 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 535) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc(OC)c(CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)C)c1) `ZINC001436200817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436200817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001436200817 none COc1ccc(OC)c(CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 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] dock color type numbers: [7, 3, 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] 0 hydrogens 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, 13, 13, 13, 20, 10, 6, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 6, 11, 11, 11, 13, 21, 21, 21, 13, 13, 20, 20, 20, 10, 10, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 106 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436200817 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436200817 Building ZINC001436229804 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436229804 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/536 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cccs1)C1Cc2ccccc2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436229804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436229804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001436229804 none O=C(N(Cc1cccs1)C1Cc2ccccc2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.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', 'C.2', 'C.2', 'Br', 'S.3', '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, 14, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [4, 1, 4, 6, 14, 22, 22, 22, 22, 8, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 22, 22, 22, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/537 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/537' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cccs1)C1Cc2ccccc2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436229804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436229804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001436229804 none O=C(N(Cc1cccs1)C1Cc2ccccc2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.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', 'C.2', 'C.2', 'Br', 'S.3', '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, 14, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [4, 1, 4, 8, 15, 22, 22, 22, 22, 10, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 22, 22, 22, 14, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3] 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436229804 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804 Building ZINC001436229804 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436229804 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 536) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N(Cc1cccs1)C1Cc2ccccc2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436229804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436229804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001436229804 none O=C(N(Cc1cccs1)C1Cc2ccccc2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.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', 'C.2', 'C.2', 'Br', 'S.3', '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, 14, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [4, 1, 4, 6, 14, 22, 22, 22, 22, 8, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 22, 22, 22, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 537) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N(Cc1cccs1)C1Cc2ccccc2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436229804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436229804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001436229804 none O=C(N(Cc1cccs1)C1Cc2ccccc2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.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', 'C.2', 'C.2', 'Br', 'S.3', '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, 14, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [4, 1, 4, 8, 15, 22, 22, 22, 22, 10, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 22, 22, 22, 14, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3] 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436229804 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436229804 Building ZINC001436232760 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436232760 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/538 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(C)cc(NC(=O)OC(C)(C)C)c2)cc1Cl) `ZINC001436232760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436232760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436232760 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(C)cc(NC(=O)OC(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.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens 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, 4, 7, 7, 7, 7, 7, 7, 22, 28, 28, 29, 29, 29, 29, 7, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 7, 7, 7, 7, 7, 22, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 2] 50 rigid atoms, others: [35, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/539 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/539' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(C)cc(NC(=O)OC(C)(C)C)c2)cc1Cl) `ZINC001436232760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436232760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436232760 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(C)cc(NC(=O)OC(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.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens 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, 4, 8, 8, 8, 8, 8, 8, 25, 31, 31, 31, 31, 31, 31, 6, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 8, 8, 8, 8, 8, 25, 31, 31, 31, 31, 31, 31, 31, 31, 31, 8, 2] 50 rigid atoms, others: [35, 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, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436232760 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760 Building ZINC001436232760 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436232760 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 538) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(C)cc(NC(=O)OC(C)(C)C)c2)cc1Cl) `ZINC001436232760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436232760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436232760 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(C)cc(NC(=O)OC(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.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens 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, 4, 7, 7, 7, 7, 7, 7, 22, 28, 28, 29, 29, 29, 29, 7, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 7, 7, 7, 7, 7, 22, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 2] 50 rigid atoms, others: [35, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 539) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(C)cc(NC(=O)OC(C)(C)C)c2)cc1Cl) `ZINC001436232760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436232760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436232760 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(C)cc(NC(=O)OC(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.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens 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, 4, 8, 8, 8, 8, 8, 8, 25, 31, 31, 31, 31, 31, 31, 6, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 8, 8, 8, 8, 8, 25, 31, 31, 31, 31, 31, 31, 31, 31, 31, 8, 2] 50 rigid atoms, others: [35, 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, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436232760 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436232760 Building ZINC001436298149 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436298149 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/540 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/540' -> `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(c1ccc(Br)cc1)C1CC1) `ZINC001436298149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436298149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001436298149 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(c1ccc(Br)cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'Br', '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'] 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, 17, 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] 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] 0 hydrogens need rotated 50 conformations in 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, 6, 11, 11, 3, 3, 1, 1, 1, 1, 5, 5, 11, 23, 23, 13, 18, 23, 23, 11, 22, 22, 3, 3, 3, 11, 11, 6, 11, 11, 3, 3, 3, 23, 23, 23, 23, 22, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 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: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/541 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/541' -> `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(c1ccc(Br)cc1)C1CC1) `ZINC001436298149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436298149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001436298149 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(c1ccc(Br)cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'Br', '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'] 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, 17, 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] 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] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 1, 1, 1, 1, 5, 5, 10, 21, 21, 13, 17, 21, 21, 10, 23, 23, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 3, 21, 21, 21, 21, 23, 23, 23, 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]) total number of confs: 137 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436298149 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149 Building ZINC001436298149 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436298149 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 540) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(c1ccc(Br)cc1)C1CC1) `ZINC001436298149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436298149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001436298149 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(c1ccc(Br)cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'Br', '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'] 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, 17, 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] 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] 0 hydrogens need rotated 50 conformations in 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, 6, 11, 11, 3, 3, 1, 1, 1, 1, 5, 5, 11, 23, 23, 13, 18, 23, 23, 11, 22, 22, 3, 3, 3, 11, 11, 6, 11, 11, 3, 3, 3, 23, 23, 23, 23, 22, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 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: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 541) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(c1ccc(Br)cc1)C1CC1) `ZINC001436298149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436298149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001436298149 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(c1ccc(Br)cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'Br', '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'] 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, 17, 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] 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] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 1, 1, 1, 1, 5, 5, 10, 21, 21, 13, 17, 21, 21, 10, 23, 23, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 3, 21, 21, 21, 21, 23, 23, 23, 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]) total number of confs: 137 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436298149 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436298149 Building ZINC001436382130 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436382130 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/542 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n2c(nnc2c2c(Cl)cccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)n1) `ZINC001436382130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436382130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001436382130 none Cc1cc(C)n2c(nnc2c2c(Cl)cccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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.2', 'C.2', 'Cl', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 24, 24, 19, 19, 19, 19, 19, 19, 19, 6, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 24, 24, 24, 24, 24, 24, 24, 24, 19, 19, 19, 6, 11, 11] 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/543 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/543' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n2c(nnc2c2c(Cl)cccc2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)n1) `ZINC001436382130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436382130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001436382130 none Cc1cc(C)n2c(nnc2c2c(Cl)cccc2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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.2', 'C.2', 'Cl', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 24, 24, 19, 19, 19, 19, 19, 19, 19, 6, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 24, 24, 24, 24, 24, 24, 24, 24, 19, 19, 19, 6, 11, 11] 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436382130 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130 Building ZINC001436382130 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436382130 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 542) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(C)n2c(nnc2c2c(Cl)cccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)n1) `ZINC001436382130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436382130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001436382130 none Cc1cc(C)n2c(nnc2c2c(Cl)cccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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.2', 'C.2', 'Cl', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 24, 24, 19, 19, 19, 19, 19, 19, 19, 6, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 24, 24, 24, 24, 24, 24, 24, 24, 19, 19, 19, 6, 11, 11] 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 543) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(C)n2c(nnc2c2c(Cl)cccc2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)n1) `ZINC001436382130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436382130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001436382130 none Cc1cc(C)n2c(nnc2c2c(Cl)cccc2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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.2', 'C.2', 'Cl', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 24, 24, 19, 19, 19, 19, 19, 19, 19, 6, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 24, 24, 24, 24, 24, 24, 24, 24, 19, 19, 19, 6, 11, 11] 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436382130 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436382130 Building ZINC001436410630 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436410630 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/544 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/544' -> `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)Nc1ccccc1OCCF) `ZINC001436410630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436410630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436410630 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1OCCF NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 12, 5, 5, 15, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 5, 5, 5, 5, 5, 5, 12, 12, 12, 3, 3, 3, 14, 14, 5, 14, 3, 3, 3, 3, 5, 5, 5, 5, 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]) total number of confs: 58 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/545 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/545' -> `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)Nc1ccccc1OCCF) `ZINC001436410630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436410630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436410630 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1OCCF NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 12, 5, 5, 15, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 5, 5, 5, 5, 5, 5, 13, 13, 13, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 3, 5, 5, 5, 5, 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]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436410630 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630 Building ZINC001436410630 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436410630 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 544) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1OCCF) `ZINC001436410630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436410630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436410630 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1OCCF NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 12, 5, 5, 15, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 5, 5, 5, 5, 5, 5, 12, 12, 12, 3, 3, 3, 14, 14, 5, 14, 3, 3, 3, 3, 5, 5, 5, 5, 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]) total number of confs: 58 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 545) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1OCCF) `ZINC001436410630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436410630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436410630 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1OCCF NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 12, 5, 5, 15, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 5, 5, 5, 5, 5, 5, 13, 13, 13, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 3, 5, 5, 5, 5, 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]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436410630 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436410630 Building ZINC001436459027 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436459027 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/546 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Br)cc1Cl) `ZINC001436459027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436459027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001436459027 none CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'Br', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27] 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/547 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/547' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Br)cc1Cl) `ZINC001436459027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436459027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001436459027 none CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'Br', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 27, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 12, 12, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28] 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436459027 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027 Building ZINC001436459027 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436459027 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 546) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Br)cc1Cl) `ZINC001436459027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436459027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001436459027 none CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'Br', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27] 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 547) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Br)cc1Cl) `ZINC001436459027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436459027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001436459027 none CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'Br', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 27, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 12, 12, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28] 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436459027 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436459027 Building ZINC001436475355 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436475355 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/548 `/scratch/xiaobo/182395/xbh-8058088.34/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)N(C)Cc1cccc(C)c1C) `ZINC001436475355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436475355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436475355 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1cccc(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'C.ar', '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'] dock atom type 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, 1, 1, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 2, 2, 5, 5, 7, 11, 11, 9, 11, 11, 11, 11, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 5, 5, 5, 7, 7, 11, 11, 9, 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, 55]) total number of confs: 69 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/549 `/scratch/xiaobo/182395/xbh-8058088.34/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)N(C)Cc1cccc(C)c1C) `ZINC001436475355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436475355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436475355 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1cccc(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'C.ar', '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'] dock atom type 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, 1, 1, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 2, 2, 5, 5, 7, 11, 11, 9, 11, 11, 11, 11, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 5, 5, 5, 7, 7, 11, 11, 9, 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, 55]) total number of confs: 67 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436475355 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355 Building ZINC001436475355 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436475355 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 548) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)N(C)Cc1cccc(C)c1C) `ZINC001436475355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436475355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436475355 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1cccc(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'C.ar', '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'] dock atom type 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, 1, 1, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 2, 2, 5, 5, 7, 11, 11, 9, 11, 11, 11, 11, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 5, 5, 5, 7, 7, 11, 11, 9, 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, 55]) total number of confs: 69 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 549) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)N(C)Cc1cccc(C)c1C) `ZINC001436475355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436475355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436475355 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1cccc(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'C.ar', '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'] dock atom type 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, 1, 1, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 2, 2, 5, 5, 7, 11, 11, 9, 11, 11, 11, 11, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 5, 5, 5, 7, 7, 11, 11, 9, 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, 55]) total number of confs: 67 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436475355 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436475355 Building ZINC001436498055 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001436498055 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/550 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 42, 42, 37, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/551 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/551' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 42, 42, 37, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/552 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/552' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 43, 43, 35, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 43, 43, 38, 43, 43, 3, 1, 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, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/553 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/553' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 43, 43, 35, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 43, 43, 38, 43, 43, 3, 1, 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, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `4' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 4 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/554 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/554' -> `4.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 40, 40, 32, 40, 40, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 40, 40, 33, 40, 40, 3, 1, 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, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `5' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 5 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/555 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/555' -> `5.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 40, 40, 32, 40, 40, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 40, 40, 33, 40, 40, 3, 1, 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, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `6' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 6 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/556 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/556' -> `6.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 42, 42, 36, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `7' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 7 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/557 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/557' -> `7.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 42, 42, 36, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436498055 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 6: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6.* 5: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3.* 7: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2.* 4: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 Building ZINC001436498055 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001436498055 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 550) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 42, 42, 37, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 551) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 42, 42, 37, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 552) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/552: 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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 43, 43, 35, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 43, 43, 38, 43, 43, 3, 1, 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, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 553) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/553: 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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 43, 43, 35, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 43, 43, 38, 43, 43, 3, 1, 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, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `4' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 4 (index: 554) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 40, 40, 32, 40, 40, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 40, 40, 33, 40, 40, 3, 1, 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, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `5' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 5 (index: 555) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 40, 40, 32, 40, 40, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 40, 40, 33, 40, 40, 3, 1, 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, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `6' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 6 (index: 556) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 42, 42, 36, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `7' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 7 (index: 557) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 42, 42, 36, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436498055 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 6: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6.* 5: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3.* 7: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2.* 4: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 Building ZINC001436498055 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001436498055 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 550) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 42, 42, 37, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 551) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 42, 42, 37, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 552) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/552: 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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 43, 43, 35, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 43, 43, 38, 43, 43, 3, 1, 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, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 553) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/553: 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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 43, 43, 35, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 43, 43, 38, 43, 43, 3, 1, 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, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `4' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 4 (index: 554) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 40, 40, 32, 40, 40, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 40, 40, 33, 40, 40, 3, 1, 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, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `5' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 5 (index: 555) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 40, 40, 32, 40, 40, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 40, 40, 33, 40, 40, 3, 1, 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, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `6' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 6 (index: 556) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 42, 42, 36, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `7' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 7 (index: 557) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 42, 42, 36, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436498055 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 6: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6.* 5: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3.* 7: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2.* 4: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 Building ZINC001436498055 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001436498055 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 550) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 42, 42, 37, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 551) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 42, 42, 37, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 552) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/552: 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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 43, 43, 35, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 43, 43, 38, 43, 43, 3, 1, 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, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 553) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/553: 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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 43, 43, 35, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 43, 43, 38, 43, 43, 3, 1, 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, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `4' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 4 (index: 554) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 40, 40, 32, 40, 40, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 40, 40, 33, 40, 40, 3, 1, 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, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `5' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 5 (index: 555) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 40, 40, 32, 40, 40, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 40, 40, 33, 40, 40, 3, 1, 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, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `6' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 6 (index: 556) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 42, 42, 36, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `7' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 7 (index: 557) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 42, 42, 36, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436498055 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 6: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6.* 5: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3.* 7: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2.* 4: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 Building ZINC001436498055 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001436498055 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 550) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 42, 42, 37, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 551) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 42, 42, 37, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 552) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/552: 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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 43, 43, 35, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 43, 43, 38, 43, 43, 3, 1, 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, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 553) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/553: 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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 43, 43, 35, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 43, 43, 38, 43, 43, 3, 1, 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, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `4' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 4 (index: 554) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 40, 40, 32, 40, 40, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 40, 40, 33, 40, 40, 3, 1, 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, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `5' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 5 (index: 555) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 40, 40, 32, 40, 40, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 40, 40, 33, 40, 40, 3, 1, 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, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `6' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 6 (index: 556) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 42, 42, 36, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `7' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 7 (index: 557) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 42, 42, 36, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436498055 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 6: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6.* 5: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3.* 7: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2.* 4: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 Building ZINC001436498055 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001436498055 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 550) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 42, 42, 37, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 551) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 42, 42, 37, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 552) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/552: 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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 43, 43, 35, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 43, 43, 38, 43, 43, 3, 1, 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, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 553) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/553: 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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 43, 43, 35, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 43, 43, 38, 43, 43, 3, 1, 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, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `4' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 4 (index: 554) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 40, 40, 32, 40, 40, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 40, 40, 33, 40, 40, 3, 1, 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, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `5' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 5 (index: 555) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 40, 40, 32, 40, 40, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 40, 40, 33, 40, 40, 3, 1, 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, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `6' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 6 (index: 556) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 42, 42, 36, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `7' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 7 (index: 557) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 42, 42, 36, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436498055 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 6: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6.* 5: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3.* 7: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2.* 4: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 Building ZINC001436498055 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001436498055 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 550) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 42, 42, 37, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 551) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 42, 42, 37, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 552) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/552: 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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 43, 43, 35, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 43, 43, 38, 43, 43, 3, 1, 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, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 553) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/553: 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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 43, 43, 35, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 43, 43, 38, 43, 43, 3, 1, 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, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `4' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 4 (index: 554) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 40, 40, 32, 40, 40, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 40, 40, 33, 40, 40, 3, 1, 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, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `5' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 5 (index: 555) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 40, 40, 32, 40, 40, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 40, 40, 33, 40, 40, 3, 1, 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, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `6' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 6 (index: 556) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 42, 42, 36, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `7' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 7 (index: 557) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 42, 42, 36, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436498055 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 6: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6.* 5: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3.* 7: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2.* 4: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 Building ZINC001436498055 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001436498055 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 550) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 42, 42, 37, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 551) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 42, 42, 37, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 552) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/552: 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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 43, 43, 35, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 43, 43, 38, 43, 43, 3, 1, 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, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 553) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/553: 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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 43, 43, 35, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 43, 43, 38, 43, 43, 3, 1, 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, 50, 51, 52]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `4' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 4 (index: 554) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 40, 40, 32, 40, 40, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 40, 40, 33, 40, 40, 3, 1, 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, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `5' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 5 (index: 555) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 40, 40, 32, 40, 40, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 40, 40, 33, 40, 40, 3, 1, 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, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `6' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 6 (index: 556) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 42, 42, 36, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `7' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 7 (index: 557) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436498055.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001436498055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001436498055 none O=C(N[C@H]1C[C@H]2CCC[C@@H](C1)N2Cc1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 42, 42, 36, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 32, 32, 42, 42, 42, 42, 42, 3, 1, 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, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436498055 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 6: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/6.* 5: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/5.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/3.* 7: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/7.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/2.* 4: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055/4.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436498055 Building ZINC001436518653 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436518653 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/558 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2cc(F)c(Br)cc21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436518653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436518653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC001436518653 none O=C(N1CCOc2cc(F)c(Br)cc21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 15, 1, 17, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 16, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 20, 20, 20, 20, 20, 20, 6, 1, 6] 26 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/559 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/559' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2cc(F)c(Br)cc21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436518653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436518653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC001436518653 none O=C(N1CCOc2cc(F)c(Br)cc21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 15, 1, 17, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 20, 20, 20, 20, 20, 20, 5, 1, 5] 25 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436518653 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653 Building ZINC001436518653 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436518653 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 558) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(F)c(Br)cc21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436518653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436518653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC001436518653 none O=C(N1CCOc2cc(F)c(Br)cc21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 15, 1, 17, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 16, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 20, 20, 20, 20, 20, 20, 6, 1, 6] 26 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 559) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(F)c(Br)cc21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436518653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436518653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC001436518653 none O=C(N1CCOc2cc(F)c(Br)cc21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 15, 1, 17, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 20, 20, 20, 20, 20, 20, 5, 1, 5] 25 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436518653 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436518653 Building ZINC001436519924 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436519924 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/560 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436519924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519924 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 5, 5, 5, 5, 5, 5, 22, 30, 30, 22, 26, 30, 30, 5, 5, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 22, 22, 30, 30, 30, 30, 5, 5, 5, 5, 8, 8] 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]) total number of confs: 169 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/561 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/561' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436519924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519924 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 5, 5, 5, 5, 5, 5, 22, 30, 30, 22, 26, 30, 30, 5, 5, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 22, 22, 30, 30, 30, 30, 5, 5, 5, 5, 8, 8] 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]) total number of confs: 169 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/562 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/562' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519924.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436519924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/2/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519924 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 6, 6, 6, 6, 6, 6, 22, 29, 29, 22, 22, 29, 29, 6, 6, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 22, 22, 29, 29, 29, 29, 6, 6, 6, 6, 8, 8] 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]) total number of confs: 149 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/563 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/563' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519924.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436519924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/3/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519924 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 6, 6, 6, 6, 6, 6, 22, 29, 29, 22, 22, 29, 29, 6, 6, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 22, 22, 29, 29, 29, 29, 6, 6, 6, 6, 8, 8] 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]) total number of confs: 149 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436519924 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 Building ZINC001436519924 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436519924 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 560) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436519924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519924 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 5, 5, 5, 5, 5, 5, 22, 30, 30, 22, 26, 30, 30, 5, 5, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 22, 22, 30, 30, 30, 30, 5, 5, 5, 5, 8, 8] 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]) total number of confs: 169 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 561) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436519924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519924 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 5, 5, 5, 5, 5, 5, 22, 30, 30, 22, 26, 30, 30, 5, 5, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 22, 22, 30, 30, 30, 30, 5, 5, 5, 5, 8, 8] 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]) total number of confs: 169 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 562) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/562: 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[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519924.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436519924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/2/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519924 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 6, 6, 6, 6, 6, 6, 22, 29, 29, 22, 22, 29, 29, 6, 6, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 22, 22, 29, 29, 29, 29, 6, 6, 6, 6, 8, 8] 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]) total number of confs: 149 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 563) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/563: 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[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519924.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436519924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/3/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519924 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 6, 6, 6, 6, 6, 6, 22, 29, 29, 22, 22, 29, 29, 6, 6, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 22, 22, 29, 29, 29, 29, 6, 6, 6, 6, 8, 8] 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]) total number of confs: 149 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436519924 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 Building ZINC001436519924 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436519924 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 560) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436519924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519924 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 5, 5, 5, 5, 5, 5, 22, 30, 30, 22, 26, 30, 30, 5, 5, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 22, 22, 30, 30, 30, 30, 5, 5, 5, 5, 8, 8] 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]) total number of confs: 169 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 561) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436519924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519924 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 5, 5, 5, 5, 5, 5, 22, 30, 30, 22, 26, 30, 30, 5, 5, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 22, 22, 30, 30, 30, 30, 5, 5, 5, 5, 8, 8] 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]) total number of confs: 169 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 562) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/562: 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[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519924.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436519924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/2/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519924 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 6, 6, 6, 6, 6, 6, 22, 29, 29, 22, 22, 29, 29, 6, 6, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 22, 22, 29, 29, 29, 29, 6, 6, 6, 6, 8, 8] 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]) total number of confs: 149 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 563) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/563: 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[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519924.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436519924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/3/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519924 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 6, 6, 6, 6, 6, 6, 22, 29, 29, 22, 22, 29, 29, 6, 6, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 22, 22, 29, 29, 29, 29, 6, 6, 6, 6, 8, 8] 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]) total number of confs: 149 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436519924 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 Building ZINC001436519924 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436519924 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 560) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436519924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519924 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 5, 5, 5, 5, 5, 5, 22, 30, 30, 22, 26, 30, 30, 5, 5, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 22, 22, 30, 30, 30, 30, 5, 5, 5, 5, 8, 8] 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]) total number of confs: 169 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 561) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436519924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519924 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 5, 5, 5, 5, 5, 5, 22, 30, 30, 22, 26, 30, 30, 5, 5, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 22, 22, 30, 30, 30, 30, 5, 5, 5, 5, 8, 8] 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]) total number of confs: 169 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 562) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/562: 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[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519924.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436519924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/2/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519924 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 6, 6, 6, 6, 6, 6, 22, 29, 29, 22, 22, 29, 29, 6, 6, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 22, 22, 29, 29, 29, 29, 6, 6, 6, 6, 8, 8] 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]) total number of confs: 149 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 563) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/563: 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[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519924.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436519924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/3/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519924 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 6, 6, 6, 6, 6, 6, 22, 29, 29, 22, 22, 29, 29, 6, 6, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 22, 22, 29, 29, 29, 29, 6, 6, 6, 6, 8, 8] 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]) total number of confs: 149 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436519924 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519924 Building ZINC001436519925 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436519925 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/564 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436519925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519925 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [9, 9, 9, 8, 8, 8, 8, 8, 8, 26, 28, 28, 26, 27, 28, 28, 8, 8, 8, 2, 8, 1, 1, 1, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 26, 26, 28, 28, 28, 28, 8, 8, 8, 8, 7, 7] 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]) total number of confs: 114 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/565 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/565' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436519925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519925 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [9, 9, 9, 8, 8, 8, 8, 8, 8, 26, 28, 28, 26, 27, 28, 28, 8, 8, 8, 2, 8, 1, 1, 1, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 26, 26, 28, 28, 28, 28, 8, 8, 8, 8, 7, 7] 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]) total number of confs: 114 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/566 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/566' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519925.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436519925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/2/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519925 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 11, 11, 11, 11, 11, 11, 30, 31, 31, 30, 30, 31, 31, 11, 11, 10, 2, 10, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 30, 30, 31, 31, 31, 31, 11, 11, 11, 11, 5, 5] 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]) total number of confs: 125 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/567 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/567' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519925.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436519925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/3/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519925 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 11, 11, 11, 11, 11, 11, 30, 31, 31, 30, 30, 31, 31, 11, 11, 10, 2, 10, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 30, 30, 31, 31, 31, 31, 11, 11, 11, 11, 5, 5] 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]) total number of confs: 125 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436519925 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 Building ZINC001436519925 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436519925 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 564) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436519925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519925 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [9, 9, 9, 8, 8, 8, 8, 8, 8, 26, 28, 28, 26, 27, 28, 28, 8, 8, 8, 2, 8, 1, 1, 1, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 26, 26, 28, 28, 28, 28, 8, 8, 8, 8, 7, 7] 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]) total number of confs: 114 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 565) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436519925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519925 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [9, 9, 9, 8, 8, 8, 8, 8, 8, 26, 28, 28, 26, 27, 28, 28, 8, 8, 8, 2, 8, 1, 1, 1, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 26, 26, 28, 28, 28, 28, 8, 8, 8, 8, 7, 7] 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]) total number of confs: 114 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 566) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/566: 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[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519925.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436519925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/2/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519925 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 11, 11, 11, 11, 11, 11, 30, 31, 31, 30, 30, 31, 31, 11, 11, 10, 2, 10, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 30, 30, 31, 31, 31, 31, 11, 11, 11, 11, 5, 5] 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]) total number of confs: 125 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 567) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/567: 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[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519925.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436519925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/3/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519925 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 11, 11, 11, 11, 11, 11, 30, 31, 31, 30, 30, 31, 31, 11, 11, 10, 2, 10, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 30, 30, 31, 31, 31, 31, 11, 11, 11, 11, 5, 5] 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]) total number of confs: 125 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436519925 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 Building ZINC001436519925 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436519925 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 564) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436519925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519925 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [9, 9, 9, 8, 8, 8, 8, 8, 8, 26, 28, 28, 26, 27, 28, 28, 8, 8, 8, 2, 8, 1, 1, 1, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 26, 26, 28, 28, 28, 28, 8, 8, 8, 8, 7, 7] 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]) total number of confs: 114 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 565) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436519925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519925 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [9, 9, 9, 8, 8, 8, 8, 8, 8, 26, 28, 28, 26, 27, 28, 28, 8, 8, 8, 2, 8, 1, 1, 1, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 26, 26, 28, 28, 28, 28, 8, 8, 8, 8, 7, 7] 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]) total number of confs: 114 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 566) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/566: 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[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519925.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436519925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/2/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519925 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 11, 11, 11, 11, 11, 11, 30, 31, 31, 30, 30, 31, 31, 11, 11, 10, 2, 10, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 30, 30, 31, 31, 31, 31, 11, 11, 11, 11, 5, 5] 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]) total number of confs: 125 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 567) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/567: 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[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519925.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436519925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/3/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519925 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 11, 11, 11, 11, 11, 11, 30, 31, 31, 30, 30, 31, 31, 11, 11, 10, 2, 10, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 30, 30, 31, 31, 31, 31, 11, 11, 11, 11, 5, 5] 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]) total number of confs: 125 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436519925 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 Building ZINC001436519925 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436519925 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 564) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436519925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519925 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [9, 9, 9, 8, 8, 8, 8, 8, 8, 26, 28, 28, 26, 27, 28, 28, 8, 8, 8, 2, 8, 1, 1, 1, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 26, 26, 28, 28, 28, 28, 8, 8, 8, 8, 7, 7] 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]) total number of confs: 114 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 565) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436519925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519925 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [9, 9, 9, 8, 8, 8, 8, 8, 8, 26, 28, 28, 26, 27, 28, 28, 8, 8, 8, 2, 8, 1, 1, 1, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 26, 26, 28, 28, 28, 28, 8, 8, 8, 8, 7, 7] 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]) total number of confs: 114 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 566) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/566: 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[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519925.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436519925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/2/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519925 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 11, 11, 11, 11, 11, 11, 30, 31, 31, 30, 30, 31, 31, 11, 11, 10, 2, 10, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 30, 30, 31, 31, 31, 31, 11, 11, 11, 11, 5, 5] 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]) total number of confs: 125 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 567) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/567: 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[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001436519925.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436519925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/3/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 55 natoms 54 natoms 53 natoms 52 names: ZINC001436519925 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [12, 12, 12, 11, 11, 11, 11, 11, 11, 30, 31, 31, 30, 30, 31, 31, 11, 11, 10, 2, 10, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 30, 30, 31, 31, 31, 31, 11, 11, 11, 11, 5, 5] 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]) total number of confs: 125 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436519925 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436519925 Building ZINC001436524557 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436524557 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/568 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436524557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436524557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436524557 none CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 25, 25, 25, 25, 43, 43, 25, 25, 43, 43, 25, 25, 13, 3, 20, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 43, 43, 43, 43, 25, 25, 25, 25, 5, 1, 5] 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]) total number of confs: 150 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/569 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/569' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436524557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436524557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436524557 none CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 25, 25, 25, 25, 43, 43, 25, 25, 43, 43, 25, 25, 13, 3, 20, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 43, 43, 43, 43, 25, 25, 25, 25, 5, 1, 5] 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]) total number of confs: 150 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/570 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/570' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436524557.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436524557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/2/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 49 natoms 48 natoms 47 natoms 46 names: ZINC001436524557 none CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 26, 26, 43, 43, 26, 26, 43, 43, 26, 26, 12, 2, 19, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 43, 43, 43, 43, 26, 26, 26, 26, 5, 1, 5] 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]) total number of confs: 146 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/571 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/571' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436524557.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436524557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/3/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 49 natoms 48 natoms 47 natoms 46 names: ZINC001436524557 none CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 26, 26, 43, 43, 26, 26, 43, 43, 26, 26, 12, 2, 19, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 43, 43, 43, 43, 26, 26, 26, 26, 5, 1, 5] 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]) total number of confs: 146 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436524557 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 Building ZINC001436524557 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436524557 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 568) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436524557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436524557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436524557 none CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 25, 25, 25, 25, 43, 43, 25, 25, 43, 43, 25, 25, 13, 3, 20, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 43, 43, 43, 43, 25, 25, 25, 25, 5, 1, 5] 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]) total number of confs: 150 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 569) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436524557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436524557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436524557 none CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 25, 25, 25, 25, 43, 43, 25, 25, 43, 43, 25, 25, 13, 3, 20, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 43, 43, 43, 43, 25, 25, 25, 25, 5, 1, 5] 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]) total number of confs: 150 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 570) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/570: 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: CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436524557.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436524557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/2/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 49 natoms 48 natoms 47 natoms 46 names: ZINC001436524557 none CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 26, 26, 43, 43, 26, 26, 43, 43, 26, 26, 12, 2, 19, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 43, 43, 43, 43, 26, 26, 26, 26, 5, 1, 5] 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]) total number of confs: 146 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 571) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/571: 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: CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436524557.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436524557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/3/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 49 natoms 48 natoms 47 natoms 46 names: ZINC001436524557 none CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 26, 26, 43, 43, 26, 26, 43, 43, 26, 26, 12, 2, 19, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 43, 43, 43, 43, 26, 26, 26, 26, 5, 1, 5] 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]) total number of confs: 146 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436524557 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 Building ZINC001436524557 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436524557 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 568) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436524557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436524557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436524557 none CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 25, 25, 25, 25, 43, 43, 25, 25, 43, 43, 25, 25, 13, 3, 20, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 43, 43, 43, 43, 25, 25, 25, 25, 5, 1, 5] 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]) total number of confs: 150 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 569) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436524557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436524557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436524557 none CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 25, 25, 25, 25, 43, 43, 25, 25, 43, 43, 25, 25, 13, 3, 20, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 43, 43, 43, 43, 25, 25, 25, 25, 5, 1, 5] 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]) total number of confs: 150 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 570) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/570: 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: CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436524557.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436524557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/2/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 49 natoms 48 natoms 47 natoms 46 names: ZINC001436524557 none CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 26, 26, 43, 43, 26, 26, 43, 43, 26, 26, 12, 2, 19, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 43, 43, 43, 43, 26, 26, 26, 26, 5, 1, 5] 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]) total number of confs: 146 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 571) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/571: 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: CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436524557.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436524557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/3/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 49 natoms 48 natoms 47 natoms 46 names: ZINC001436524557 none CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 26, 26, 43, 43, 26, 26, 43, 43, 26, 26, 12, 2, 19, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 43, 43, 43, 43, 26, 26, 26, 26, 5, 1, 5] 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]) total number of confs: 146 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436524557 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 Building ZINC001436524557 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436524557 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 568) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436524557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436524557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436524557 none CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 25, 25, 25, 25, 43, 43, 25, 25, 43, 43, 25, 25, 13, 3, 20, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 43, 43, 43, 43, 25, 25, 25, 25, 5, 1, 5] 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]) total number of confs: 150 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 569) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436524557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436524557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001436524557 none CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 25, 25, 25, 25, 43, 43, 25, 25, 43, 43, 25, 25, 13, 3, 20, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 43, 43, 43, 43, 25, 25, 25, 25, 5, 1, 5] 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]) total number of confs: 150 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 570) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/570: 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: CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436524557.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436524557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/2/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 49 natoms 48 natoms 47 natoms 46 names: ZINC001436524557 none CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 26, 26, 43, 43, 26, 26, 43, 43, 26, 26, 12, 2, 19, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 43, 43, 43, 43, 26, 26, 26, 26, 5, 1, 5] 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]) total number of confs: 146 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 571) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/571: 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: CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001436524557.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436524557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/3/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 49 natoms 48 natoms 47 natoms 46 names: ZINC001436524557 none CC1(C)CN(c2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 26, 26, 43, 43, 26, 26, 43, 43, 26, 26, 12, 2, 19, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 43, 43, 43, 43, 26, 26, 26, 26, 5, 1, 5] 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]) total number of confs: 146 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436524557 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436524557 Building ZINC001436563466 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436563466 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/572 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001436563466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436563466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436563466 none C[C@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 7, 8, 20, 20, 15, 15, 20, 20, 20, 20, 20, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 42 rigid atoms, others: [24, 22, 23] set([0, 1, 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]) total number of confs: 86 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/573 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/573' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001436563466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436563466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436563466 none C[C@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 10, 12, 24, 24, 19, 20, 24, 24, 24, 24, 24, 12, 12, 12, 12, 8, 2, 8, 1, 1, 1, 10, 10, 16, 16, 10, 16, 16, 16, 12, 12, 12, 12, 12, 24, 24, 24, 24, 12, 12, 12, 12, 12, 10, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 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]) total number of confs: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436563466 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466 Building ZINC001436563466 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436563466 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 572) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001436563466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436563466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436563466 none C[C@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 7, 8, 20, 20, 15, 15, 20, 20, 20, 20, 20, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 42 rigid atoms, others: [24, 22, 23] set([0, 1, 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]) total number of confs: 86 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 573) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001436563466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436563466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436563466 none C[C@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 10, 12, 24, 24, 19, 20, 24, 24, 24, 24, 24, 12, 12, 12, 12, 8, 2, 8, 1, 1, 1, 10, 10, 16, 16, 10, 16, 16, 16, 12, 12, 12, 12, 12, 24, 24, 24, 24, 12, 12, 12, 12, 12, 10, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 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]) total number of confs: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436563466 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563466 Building ZINC001436563467 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436563467 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/574 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001436563467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436563467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436563467 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 22, 22, 19, 22, 22, 22, 22, 22, 22, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 8, 8, 14, 14, 8, 14, 14, 14, 10, 10, 10, 10, 10, 22, 22, 22, 22, 10, 10, 10, 10, 10, 8, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/575 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/575' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001436563467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436563467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436563467 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 8, 9, 23, 23, 9, 16, 23, 23, 23, 23, 23, 9, 9, 9, 9, 6, 2, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 23, 23, 23, 23, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 8, 8, 8] 44 rigid atoms, others: [24, 22, 23] set([0, 1, 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]) total number of confs: 132 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436563467 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467 Building ZINC001436563467 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436563467 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 574) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001436563467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436563467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436563467 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 22, 22, 19, 22, 22, 22, 22, 22, 22, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 8, 8, 14, 14, 8, 14, 14, 14, 10, 10, 10, 10, 10, 22, 22, 22, 22, 10, 10, 10, 10, 10, 8, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 575) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001436563467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436563467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436563467 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 8, 9, 23, 23, 9, 16, 23, 23, 23, 23, 23, 9, 9, 9, 9, 6, 2, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 23, 23, 23, 23, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 8, 8, 8] 44 rigid atoms, others: [24, 22, 23] set([0, 1, 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]) total number of confs: 132 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436563467 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563467 Building ZINC001436563468 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436563468 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/576 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001436563468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436563468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436563468 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 14, 26, 26, 22, 26, 26, 26, 26, 26, 26, 14, 14, 14, 14, 7, 1, 12, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 14, 14, 14, 14, 14, 26, 26, 26, 26, 14, 14, 14, 14, 14, 6, 8, 8, 8, 8, 8, 8, 8, 8] 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: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/577 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/577' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001436563468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436563468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436563468 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 13, 13, 13, 13, 7, 1, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 26, 26, 26, 26, 13, 13, 13, 13, 13, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436563468 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468 Building ZINC001436563468 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436563468 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 576) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001436563468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436563468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436563468 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 14, 26, 26, 22, 26, 26, 26, 26, 26, 26, 14, 14, 14, 14, 7, 1, 12, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 14, 14, 14, 14, 14, 26, 26, 26, 26, 14, 14, 14, 14, 14, 6, 8, 8, 8, 8, 8, 8, 8, 8] 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: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 577) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/577: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001436563468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436563468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436563468 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 13, 13, 13, 13, 7, 1, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 26, 26, 26, 26, 13, 13, 13, 13, 13, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436563468 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436563468 Building ZINC001436573109 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436573109 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/578 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21) `ZINC001436573109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436573109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001436573109 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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: [48, 48, 48, 48, 29, 13, 29, 13, 13, 13, 9, 2, 12, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 48, 48, 48, 48, 48, 48, 48, 48, 48, 13, 13, 13, 13, 3, 3, 3, 13, 13, 13, 13] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/579 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/579' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21) `ZINC001436573109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436573109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001436573109 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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: [47, 47, 47, 47, 30, 15, 30, 15, 15, 15, 12, 2, 15, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 47, 47, 47, 47, 47, 47, 47, 47, 47, 15, 15, 15, 15, 3, 1, 3, 15, 15, 15, 15] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436573109 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109 Building ZINC001436573109 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436573109 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 578) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21) `ZINC001436573109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436573109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001436573109 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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: [48, 48, 48, 48, 29, 13, 29, 13, 13, 13, 9, 2, 12, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 48, 48, 48, 48, 48, 48, 48, 48, 48, 13, 13, 13, 13, 3, 3, 3, 13, 13, 13, 13] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 579) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21) `ZINC001436573109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436573109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001436573109 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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: [47, 47, 47, 47, 30, 15, 30, 15, 15, 15, 12, 2, 15, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 47, 47, 47, 47, 47, 47, 47, 47, 47, 15, 15, 15, 15, 3, 1, 3, 15, 15, 15, 15] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436573109 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436573109 Building ZINC001436646890 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436646890 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/580 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(CCCN2CCCC2)c2ccc(Cl)cc2)cc1Cl) `ZINC001436646890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436646890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436646890 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(CCCN2CCCC2)c2ccc(Cl)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.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 1, 1, 1, 1, 16, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 6, 6, 1, 1, 1, 1, 2, 2, 3, 5, 6, 13, 21, 21, 21, 20, 3, 6, 6, 4, 6, 6, 6, 6, 6, 6, 14, 14, 14, 6, 6, 5, 5, 6, 6, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/581 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/581' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(CCCN2CCCC2)c2ccc(Cl)cc2)cc1Cl) `ZINC001436646890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436646890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436646890 none COc1ccc([C@]([O-])([SiH3])C(=O)N(CCCN2CCCC2)c2ccc(Cl)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.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 1, 1, 1, 1, 16, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 3, 5, 6, 14, 22, 22, 22, 22, 3, 8, 8, 8, 8, 8, 8, 6, 6, 6, 13, 13, 13, 6, 6, 5, 5, 6, 6, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 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, 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/182395/xbh-8058088.34/working/building/ZINC001436646890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436646890 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890 Building ZINC001436646890 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436646890 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 580) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N(CCCN2CCCC2)c2ccc(Cl)cc2)cc1Cl) `ZINC001436646890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436646890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436646890 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(CCCN2CCCC2)c2ccc(Cl)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.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 1, 1, 1, 1, 16, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 6, 6, 1, 1, 1, 1, 2, 2, 3, 5, 6, 13, 21, 21, 21, 20, 3, 6, 6, 4, 6, 6, 6, 6, 6, 6, 14, 14, 14, 6, 6, 5, 5, 6, 6, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 581) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N(CCCN2CCCC2)c2ccc(Cl)cc2)cc1Cl) `ZINC001436646890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436646890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001436646890 none COc1ccc([C@]([O-])([SiH3])C(=O)N(CCCN2CCCC2)c2ccc(Cl)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.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 1, 1, 1, 1, 16, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 3, 5, 6, 14, 22, 22, 22, 22, 3, 8, 8, 8, 8, 8, 8, 6, 6, 6, 13, 13, 13, 6, 6, 5, 5, 6, 6, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 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, 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/182395/xbh-8058088.34/working/building/ZINC001436646890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001436646890 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001436646890 Building ZINC001437025602 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437025602 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/582 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Br)cc1C1(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001437025602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437025602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001437025602 none COc1ccc(Br)cc1C1(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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, 4, 9, 6, 8, 10, 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: [32, 23, 23, 23, 10, 23, 23, 23, 10, 6, 6, 1, 6, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 10, 10, 32, 32, 32, 23, 23, 23, 6, 6, 6, 6, 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]) total number of confs: 125 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/583 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/583' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Br)cc1C1(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001437025602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437025602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001437025602 none COc1ccc(Br)cc1C1(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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, 4, 9, 6, 8, 10, 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: [32, 23, 23, 23, 15, 23, 23, 23, 10, 6, 6, 1, 6, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 10, 10, 32, 32, 32, 23, 23, 23, 6, 6, 1, 6, 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]) total number of confs: 115 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437025602 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602 Building ZINC001437025602 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437025602 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 582) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc(Br)cc1C1(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001437025602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437025602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001437025602 none COc1ccc(Br)cc1C1(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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, 4, 9, 6, 8, 10, 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: [32, 23, 23, 23, 10, 23, 23, 23, 10, 6, 6, 1, 6, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 10, 10, 32, 32, 32, 23, 23, 23, 6, 6, 6, 6, 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]) total number of confs: 125 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 583) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc(Br)cc1C1(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001437025602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437025602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001437025602 none COc1ccc(Br)cc1C1(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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, 4, 9, 6, 8, 10, 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: [32, 23, 23, 23, 15, 23, 23, 23, 10, 6, 6, 1, 6, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 10, 10, 32, 32, 32, 23, 23, 23, 6, 6, 1, 6, 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]) total number of confs: 115 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437025602 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437025602 Building ZINC001437084017 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437084017 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/584 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(COc2cccc(F)c2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001437084017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437084017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001437084017 none O=C(NCc1ccc(COc2cccc(F)c2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 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] 0 hydrogens need 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, 6, 9, 9, 8, 9, 27, 27, 50, 50, 50, 50, 50, 50, 9, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 9, 9, 27, 27, 50, 50, 50, 50, 9, 9, 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/585 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/585' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(COc2cccc(F)c2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001437084017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437084017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001437084017 none O=C(NCc1ccc(COc2cccc(F)c2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 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] 0 hydrogens 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, 8, 8, 8, 8, 27, 27, 50, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 27, 27, 50, 50, 50, 50, 8, 8, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 40, 41, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437084017 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017 Building ZINC001437084017 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437084017 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 584) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1ccc(COc2cccc(F)c2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001437084017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437084017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001437084017 none O=C(NCc1ccc(COc2cccc(F)c2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 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] 0 hydrogens need 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, 6, 9, 9, 8, 9, 27, 27, 50, 50, 50, 50, 50, 50, 9, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 9, 9, 27, 27, 50, 50, 50, 50, 9, 9, 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 585) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1ccc(COc2cccc(F)c2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001437084017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437084017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001437084017 none O=C(NCc1ccc(COc2cccc(F)c2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 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] 0 hydrogens 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, 8, 8, 8, 8, 27, 27, 50, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 27, 27, 50, 50, 50, 50, 8, 8, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 40, 41, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437084017 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437084017 Building ZINC001437175006 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437175006 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/586 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c(Cl)c1) `ZINC001437175006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437175006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC001437175006 none CC(=O)Nc1cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 16, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 34, 6, 6, 13, 13, 13, 6, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 13, 13, 13, 34, 34, 34, 34, 13, 6, 11, 11, 13] 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/587 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/587' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c(Cl)c1) `ZINC001437175006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437175006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC001437175006 none CC(=O)Nc1cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 16, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 23, 11, 23, 23, 23, 6, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 23, 23, 23, 33, 33, 33, 33, 23, 6, 11, 11, 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437175006 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006 Building ZINC001437175006 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437175006 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 586) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(=O)Nc1cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c(Cl)c1) `ZINC001437175006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437175006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC001437175006 none CC(=O)Nc1cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 16, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 34, 6, 6, 13, 13, 13, 6, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 13, 13, 13, 34, 34, 34, 34, 13, 6, 11, 11, 13] 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 587) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(=O)Nc1cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c(Cl)c1) `ZINC001437175006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437175006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC001437175006 none CC(=O)Nc1cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 16, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 23, 11, 23, 23, 23, 6, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 23, 23, 23, 33, 33, 33, 33, 23, 6, 11, 11, 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437175006 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437175006 Building ZINC001437285620 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437285620 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/588 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2cc(F)cc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)c2)C[C@H](C)O1) `ZINC001437285620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437285620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001437285620 none C[C@@H]1CN(c2cc(F)cc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)c2)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 5, 5, 7, 5, 12, 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, 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] 0 hydrogens 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, 19, 13, 13, 13, 13, 13, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 13, 13, 2, 3, 1, 3, 13, 46, 46, 46, 46, 46] 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/589 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/589' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2cc(F)cc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)c2)C[C@H](C)O1) `ZINC001437285620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437285620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001437285620 none C[C@@H]1CN(c2cc(F)cc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)c2)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 5, 5, 7, 5, 12, 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, 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] 0 hydrogens 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, 20, 14, 14, 14, 14, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 14, 14, 2, 3, 1, 3, 14, 46, 46, 46, 46, 46] 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437285620 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620 Building ZINC001437285620 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437285620 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 588) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@H]1CN(c2cc(F)cc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)c2)C[C@H](C)O1) `ZINC001437285620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437285620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001437285620 none C[C@@H]1CN(c2cc(F)cc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)c2)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 5, 5, 7, 5, 12, 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, 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] 0 hydrogens 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, 19, 13, 13, 13, 13, 13, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 13, 13, 2, 3, 1, 3, 13, 46, 46, 46, 46, 46] 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 589) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@H]1CN(c2cc(F)cc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)c2)C[C@H](C)O1) `ZINC001437285620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437285620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001437285620 none C[C@@H]1CN(c2cc(F)cc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)c2)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 5, 5, 7, 5, 12, 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, 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] 0 hydrogens 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, 20, 14, 14, 14, 14, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 14, 14, 2, 3, 1, 3, 14, 46, 46, 46, 46, 46] 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437285620 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437285620 Building ZINC001437299839 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437299839 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/590 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/590' -> `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]1CCc2ccc(C)cc21) `ZINC001437299839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437299839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001437299839 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCc2ccc(C)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', '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'] dock atom type 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, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 1, 3, 3, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 24, 24, 8, 24, 3, 3, 3, 3, 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]) total number of confs: 92 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/591 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/591' -> `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]1CCc2ccc(C)cc21) `ZINC001437299839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437299839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001437299839 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCc2ccc(C)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', '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'] dock atom type 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, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 6, 6, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 14, 14, 6, 14, 2, 2, 2, 6, 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]) total number of confs: 73 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437299839 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839 Building ZINC001437299839 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437299839 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 590) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCc2ccc(C)cc21) `ZINC001437299839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437299839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001437299839 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCc2ccc(C)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', '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'] dock atom type 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, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 1, 3, 3, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 24, 24, 8, 24, 3, 3, 3, 3, 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]) total number of confs: 92 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 591) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCc2ccc(C)cc21) `ZINC001437299839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437299839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001437299839 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCc2ccc(C)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', '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'] dock atom type 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, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 6, 6, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 14, 14, 6, 14, 2, 2, 2, 6, 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]) total number of confs: 73 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437299839 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299839 Building ZINC001437299847 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437299847 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/592 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/592' -> `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]1CCc2ccc(C)cc21) `ZINC001437299847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437299847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001437299847 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCc2ccc(C)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', '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'] dock atom type 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, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 17, 17, 4, 17, 3, 3, 3, 5, 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]) total number of confs: 71 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/593 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/593' -> `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]1CCc2ccc(C)cc21) `ZINC001437299847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437299847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001437299847 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCc2ccc(C)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', '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'] dock atom type 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, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 4, 4, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 22, 22, 9, 22, 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]) total number of confs: 91 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437299847 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847 Building ZINC001437299847 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437299847 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 592) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCc2ccc(C)cc21) `ZINC001437299847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437299847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001437299847 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCc2ccc(C)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', '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'] dock atom type 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, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 17, 17, 4, 17, 3, 3, 3, 5, 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]) total number of confs: 71 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 593) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCc2ccc(C)cc21) `ZINC001437299847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437299847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001437299847 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCc2ccc(C)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', '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'] dock atom type 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, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 4, 4, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 22, 22, 9, 22, 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]) total number of confs: 91 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437299847 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437299847 Building ZINC001437343795 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437343795 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/594 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(Oc2ccccc2F)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001437343795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437343795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001437343795 none O=C(NCc1cccc(Oc2ccccc2F)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 12, 1, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 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] 0 hydrogens need 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, 22, 22, 22, 22, 22, 46, 49, 49, 49, 49, 49, 49, 19, 1, 1, 1, 3, 3, 3, 3, 3, 2, 8, 8, 22, 22, 22, 49, 49, 49, 49, 22, 3, 3] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/595 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/595' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(Oc2ccccc2F)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001437343795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437343795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001437343795 none O=C(NCc1cccc(Oc2ccccc2F)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 12, 1, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 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] 0 hydrogens need 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, 23, 23, 23, 23, 23, 46, 49, 49, 49, 49, 49, 49, 22, 1, 1, 1, 3, 3, 3, 3, 3, 2, 8, 8, 23, 23, 23, 49, 49, 49, 49, 23, 3, 3] 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437343795 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795 Building ZINC001437343795 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437343795 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 594) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1cccc(Oc2ccccc2F)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001437343795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437343795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001437343795 none O=C(NCc1cccc(Oc2ccccc2F)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 12, 1, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 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] 0 hydrogens need 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, 22, 22, 22, 22, 22, 46, 49, 49, 49, 49, 49, 49, 19, 1, 1, 1, 3, 3, 3, 3, 3, 2, 8, 8, 22, 22, 22, 49, 49, 49, 49, 22, 3, 3] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 595) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1cccc(Oc2ccccc2F)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001437343795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437343795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001437343795 none O=C(NCc1cccc(Oc2ccccc2F)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 12, 1, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 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] 0 hydrogens need 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, 23, 23, 23, 23, 23, 46, 49, 49, 49, 49, 49, 49, 22, 1, 1, 1, 3, 3, 3, 3, 3, 2, 8, 8, 23, 23, 23, 49, 49, 49, 49, 23, 3, 3] 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437343795 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437343795 Building ZINC001437462749 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437462749 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/596 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1ccc(C[C@@]2(C)CCCN2C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1) `ZINC001437462749.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437462749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001437462749 none CC(C)(C)c1ccc(C[C@@]2(C)CCCN2C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 17, 17, 17, 17, 8, 8, 8, 8, 8, 8, 3, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 17, 17, 24, 24, 24, 24, 24, 24, 24, 24, 24, 17, 17, 17, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 11, 11, 6, 11, 11, 6, 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, 58, 59, 60, 61, 62]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/597 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/597' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1ccc(C[C@@]2(C)CCCN2C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1) `ZINC001437462749.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437462749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001437462749 none CC(C)(C)c1ccc(C[C@@]2(C)CCCN2C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 27, 27, 16, 17, 17, 16, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 16, 16, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 8, 8, 6, 8, 8, 6, 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, 58, 59, 60, 61, 62]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437462749 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749 Building ZINC001437462749 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437462749 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 596) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)c1ccc(C[C@@]2(C)CCCN2C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1) `ZINC001437462749.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437462749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001437462749 none CC(C)(C)c1ccc(C[C@@]2(C)CCCN2C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 17, 17, 17, 17, 8, 8, 8, 8, 8, 8, 3, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 17, 17, 24, 24, 24, 24, 24, 24, 24, 24, 24, 17, 17, 17, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 11, 11, 6, 11, 11, 6, 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, 58, 59, 60, 61, 62]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 597) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)c1ccc(C[C@@]2(C)CCCN2C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1) `ZINC001437462749.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437462749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001437462749 none CC(C)(C)c1ccc(C[C@@]2(C)CCCN2C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 27, 27, 16, 17, 17, 16, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 16, 16, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 8, 8, 6, 8, 8, 6, 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, 58, 59, 60, 61, 62]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437462749 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462749 Building ZINC001437462750 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437462750 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/598 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1ccc(C[C@]2(C)CCCN2C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1) `ZINC001437462750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437462750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001437462750 none CC(C)(C)c1ccc(C[C@]2(C)CCCN2C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 18, 18, 18, 17, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 18, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 17, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 8, 8, 6, 8, 8, 6, 18, 18] 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, 59, 60, 61, 62]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/599 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/599' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1ccc(C[C@]2(C)CCCN2C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1) `ZINC001437462750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437462750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001437462750 none CC(C)(C)c1ccc(C[C@]2(C)CCCN2C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 25, 25, 18, 18, 18, 18, 8, 8, 8, 8, 8, 8, 3, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 18, 18, 25, 25, 25, 25, 25, 25, 25, 25, 25, 18, 18, 18, 18, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 11, 11, 6, 11, 11, 6, 18, 18] 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, 59, 60, 61, 62]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437462750 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750 Building ZINC001437462750 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437462750 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 598) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)c1ccc(C[C@]2(C)CCCN2C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1) `ZINC001437462750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437462750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001437462750 none CC(C)(C)c1ccc(C[C@]2(C)CCCN2C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 18, 18, 18, 17, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 18, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 17, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 8, 8, 6, 8, 8, 6, 18, 18] 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, 59, 60, 61, 62]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 599) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)c1ccc(C[C@]2(C)CCCN2C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1) `ZINC001437462750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437462750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001437462750 none CC(C)(C)c1ccc(C[C@]2(C)CCCN2C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 25, 25, 18, 18, 18, 18, 8, 8, 8, 8, 8, 8, 3, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 18, 18, 25, 25, 25, 25, 25, 25, 25, 25, 25, 18, 18, 18, 18, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 11, 11, 6, 11, 11, 6, 18, 18] 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, 59, 60, 61, 62]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437462750 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437462750 Building ZINC001437489329 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437489329 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/600 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(c2ccc(Cl)s2)nn1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001437489329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437489329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC001437489329 none O=C(Nc1ccc(c2ccc(Cl)s2)nn1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 8, 8, 8, 8, 34, 34, 34, 34, 34, 8, 8, 1, 1, 1, 11, 11, 11, 11, 11, 6, 8, 8, 34, 34, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/601 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/601' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(c2ccc(Cl)s2)nn1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001437489329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437489329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC001437489329 none O=C(Nc1ccc(c2ccc(Cl)s2)nn1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 8, 8, 8, 8, 36, 36, 36, 36, 36, 8, 8, 1, 1, 1, 10, 10, 10, 10, 10, 6, 8, 8, 36, 36, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437489329 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329 Building ZINC001437489329 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437489329 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 600) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1ccc(c2ccc(Cl)s2)nn1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001437489329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437489329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC001437489329 none O=C(Nc1ccc(c2ccc(Cl)s2)nn1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 8, 8, 8, 8, 34, 34, 34, 34, 34, 8, 8, 1, 1, 1, 11, 11, 11, 11, 11, 6, 8, 8, 34, 34, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 601) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1ccc(c2ccc(Cl)s2)nn1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001437489329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437489329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC001437489329 none O=C(Nc1ccc(c2ccc(Cl)s2)nn1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 8, 8, 8, 8, 36, 36, 36, 36, 36, 8, 8, 1, 1, 1, 10, 10, 10, 10, 10, 6, 8, 8, 36, 36, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437489329 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437489329 Building ZINC001437512200 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437512200 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/602 `/scratch/xiaobo/182395/xbh-8058088.34/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)NC[C@H]1C[C@H](C)C[C@H](C)C1) `ZINC001437512200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437512200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001437512200 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](C)C[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', 'H', 'C.3', 'C.3', 'H', 'C.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', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 7, 5, 5, 5, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 12, 12, 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, 58]) total number of confs: 75 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/603 `/scratch/xiaobo/182395/xbh-8058088.34/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)NC[C@H]1C[C@H](C)C[C@H](C)C1) `ZINC001437512200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437512200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001437512200 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](C)C[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', 'H', 'C.3', 'C.3', 'H', 'C.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', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 7, 5, 5, 5, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 11, 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, 58]) total number of confs: 72 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437512200 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200 Building ZINC001437512200 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437512200 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 602) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)NC[C@H]1C[C@H](C)C[C@H](C)C1) `ZINC001437512200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437512200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001437512200 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](C)C[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', 'H', 'C.3', 'C.3', 'H', 'C.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', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 7, 5, 5, 5, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 12, 12, 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, 58]) total number of confs: 75 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 603) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)NC[C@H]1C[C@H](C)C[C@H](C)C1) `ZINC001437512200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437512200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001437512200 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](C)C[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', 'H', 'C.3', 'C.3', 'H', 'C.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', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 7, 5, 5, 5, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 11, 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, 58]) total number of confs: 72 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437512200 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512200 Building ZINC001437512202 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437512202 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/604 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/604' -> `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)NCC1C[C@@H](C)C[C@H](C)C1) `ZINC001437512202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437512202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001437512202 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1C[C@@H](C)C[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', 'C.3', 'C.3', 'H', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 4, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 7, 7, 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, 58]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/605 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/605' -> `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)NCC1C[C@@H](C)C[C@H](C)C1) `ZINC001437512202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437512202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001437512202 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1C[C@@H](C)C[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', 'C.3', 'C.3', 'H', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 2, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 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: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437512202 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202 Building ZINC001437512202 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437512202 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 604) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1C[C@@H](C)C[C@H](C)C1) `ZINC001437512202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437512202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001437512202 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1C[C@@H](C)C[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', 'C.3', 'C.3', 'H', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 4, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 7, 7, 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, 58]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 605) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1C[C@@H](C)C[C@H](C)C1) `ZINC001437512202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437512202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001437512202 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1C[C@@H](C)C[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', 'C.3', 'C.3', 'H', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 2, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 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: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437512202 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512202 Building ZINC001437512204 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437512204 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/606 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/606' -> `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)NCC1C[C@H](C)C[C@@H](C)C1) `ZINC001437512204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437512204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001437512204 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1C[C@H](C)C[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', 'C.3', 'C.3', 'H', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 2, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 5, 8, 2, 2, 2, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/607 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/607' -> `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)NCC1C[C@H](C)C[C@@H](C)C1) `ZINC001437512204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437512204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001437512204 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1C[C@H](C)C[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', 'C.3', 'C.3', 'H', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 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, 58]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437512204 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204 Building ZINC001437512204 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437512204 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 606) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1C[C@H](C)C[C@@H](C)C1) `ZINC001437512204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437512204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001437512204 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1C[C@H](C)C[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', 'C.3', 'C.3', 'H', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 2, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 5, 8, 2, 2, 2, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 607) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1C[C@H](C)C[C@@H](C)C1) `ZINC001437512204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437512204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001437512204 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1C[C@H](C)C[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', 'C.3', 'C.3', 'H', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 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, 58]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437512204 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437512204 Building ZINC001437708308 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437708308 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/608 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC001437708308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437708308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001437708308 none CCC(=O)c1ccc(NC(=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', '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', '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, 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, 1, 1, 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, 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] 0 hydrogens 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, 12, 6, 12, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 6, 6, 13, 13, 13, 13, 13, 6, 6, 2, 2, 2, 2, 9, 9, 4, 9, 2, 2, 2, 6, 6] 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: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/609 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/609' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC001437708308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437708308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001437708308 none CCC(=O)c1ccc(NC(=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', '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', '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, 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, 1, 1, 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, 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] 0 hydrogens 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, 2, 10, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 6, 6, 14, 14, 14, 14, 14, 6, 6, 2, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 6, 6] 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437708308 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308 Building ZINC001437708308 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437708308 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 608) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC001437708308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437708308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001437708308 none CCC(=O)c1ccc(NC(=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', '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', '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, 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, 1, 1, 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, 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] 0 hydrogens 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, 12, 6, 12, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 6, 6, 13, 13, 13, 13, 13, 6, 6, 2, 2, 2, 2, 9, 9, 4, 9, 2, 2, 2, 6, 6] 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: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 609) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC001437708308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437708308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001437708308 none CCC(=O)c1ccc(NC(=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', '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', '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, 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, 1, 1, 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, 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] 0 hydrogens 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, 2, 10, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 6, 6, 14, 14, 14, 14, 14, 6, 6, 2, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 6, 6] 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437708308 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437708308 Building ZINC001437752835 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437752835 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/610 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CO[C@@H](c2cccc(Cl)c2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001437752835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437752835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001437752835 none CC1(C)CO[C@@H](c2cccc(Cl)c2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 7, 1, 1, 1, 1, 1, 16, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 32, 32, 30, 32, 32, 32, 9, 8, 2, 8, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 32, 32, 32, 32, 9, 9, 4, 4] 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]) total number of confs: 63 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/611 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/611' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CO[C@@H](c2cccc(Cl)c2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001437752835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437752835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001437752835 none CC1(C)CO[C@@H](c2cccc(Cl)c2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 7, 1, 1, 1, 1, 1, 16, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 30, 30, 26, 30, 30, 30, 7, 6, 2, 6, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 30, 30, 30, 30, 7, 7, 4, 4] 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]) total number of confs: 61 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437752835 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835 Building ZINC001437752835 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437752835 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 610) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC1(C)CO[C@@H](c2cccc(Cl)c2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001437752835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437752835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001437752835 none CC1(C)CO[C@@H](c2cccc(Cl)c2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 7, 1, 1, 1, 1, 1, 16, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 32, 32, 30, 32, 32, 32, 9, 8, 2, 8, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 32, 32, 32, 32, 9, 9, 4, 4] 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]) total number of confs: 63 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 611) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC1(C)CO[C@@H](c2cccc(Cl)c2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001437752835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437752835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001437752835 none CC1(C)CO[C@@H](c2cccc(Cl)c2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 7, 1, 1, 1, 1, 1, 16, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 30, 30, 26, 30, 30, 30, 7, 6, 2, 6, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 30, 30, 30, 30, 7, 7, 4, 4] 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]) total number of confs: 61 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437752835 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752835 Building ZINC001437752836 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437752836 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/612 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CO[C@H](c2cccc(Cl)c2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001437752836.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437752836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001437752836 none CC1(C)CO[C@H](c2cccc(Cl)c2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 7, 1, 1, 1, 1, 1, 16, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 6, 5, 2, 5, 1, 1, 1, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 6, 6, 5, 5] 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]) total number of confs: 49 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/613 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/613' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CO[C@H](c2cccc(Cl)c2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001437752836.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437752836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001437752836 none CC1(C)CO[C@H](c2cccc(Cl)c2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 7, 1, 1, 1, 1, 1, 16, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 9, 7, 3, 7, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 32, 32, 32, 32, 9, 9, 4, 4] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437752836 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836 Building ZINC001437752836 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437752836 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 612) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC1(C)CO[C@H](c2cccc(Cl)c2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001437752836.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437752836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001437752836 none CC1(C)CO[C@H](c2cccc(Cl)c2)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 7, 1, 1, 1, 1, 1, 16, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 6, 5, 2, 5, 1, 1, 1, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 6, 6, 5, 5] 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]) total number of confs: 49 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 613) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC1(C)CO[C@H](c2cccc(Cl)c2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001437752836.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437752836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001437752836 none CC1(C)CO[C@H](c2cccc(Cl)c2)CN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 7, 1, 1, 1, 1, 1, 16, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 9, 7, 3, 7, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 32, 32, 32, 32, 9, 9, 4, 4] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001437752836 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001437752836 Building ZINC001438057323 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438057323 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/614 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)c(Br)cc1F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001438057323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438057323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 28 natoms 27 natoms 26 natoms 25 names: ZINC001438057323 none O=C(Nc1cc(Cl)c(Br)cc1F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 17, 1, 1, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 25, 25, 25, 19, 19, 25, 25, 25, 1, 1, 1, 12, 12, 12, 12, 12, 6, 25, 25, 12, 12] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/615 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/615' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)c(Br)cc1F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001438057323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438057323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 28 natoms 27 natoms 26 natoms 25 names: ZINC001438057323 none O=C(Nc1cc(Cl)c(Br)cc1F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 17, 1, 1, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 26, 26, 26, 19, 23, 26, 26, 26, 1, 1, 1, 12, 12, 12, 12, 12, 6, 26, 26, 12, 12] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438057323 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323 Building ZINC001438057323 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438057323 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 614) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cc(Cl)c(Br)cc1F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001438057323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438057323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 28 natoms 27 natoms 26 natoms 25 names: ZINC001438057323 none O=C(Nc1cc(Cl)c(Br)cc1F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 17, 1, 1, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 25, 25, 25, 19, 19, 25, 25, 25, 1, 1, 1, 12, 12, 12, 12, 12, 6, 25, 25, 12, 12] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 615) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cc(Cl)c(Br)cc1F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001438057323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438057323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 28 natoms 27 natoms 26 natoms 25 names: ZINC001438057323 none O=C(Nc1cc(Cl)c(Br)cc1F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 17, 1, 1, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 26, 26, 26, 19, 23, 26, 26, 26, 1, 1, 1, 12, 12, 12, 12, 12, 6, 26, 26, 12, 12] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438057323 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438057323 Building ZINC001438097642 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438097642 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/616 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCCCC1) `ZINC001438097642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438097642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001438097642 none CC(C)(C)OC(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 30, 41, 18, 11, 7, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 11, 11, 48, 48, 48, 48, 48, 48, 48, 48, 48, 30, 18, 18, 4, 3, 1, 3, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/617 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/617' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCCCC1) `ZINC001438097642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438097642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001438097642 none CC(C)(C)OC(=O)NCC1(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 28, 40, 18, 10, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 10, 10, 10, 10, 48, 48, 48, 48, 48, 48, 48, 48, 48, 28, 18, 18, 3, 3, 1, 3, 10, 10, 10, 10, 10, 10, 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]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438097642 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642 Building ZINC001438097642 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438097642 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 616) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)OC(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCCCC1) `ZINC001438097642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438097642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001438097642 none CC(C)(C)OC(=O)NCC1(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 30, 41, 18, 11, 7, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 11, 11, 48, 48, 48, 48, 48, 48, 48, 48, 48, 30, 18, 18, 4, 3, 1, 3, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 617) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)OC(=O)NCC1(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCCCC1) `ZINC001438097642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438097642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001438097642 none CC(C)(C)OC(=O)NCC1(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 28, 40, 18, 10, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 10, 10, 10, 10, 48, 48, 48, 48, 48, 48, 48, 48, 48, 28, 18, 18, 3, 3, 1, 3, 10, 10, 10, 10, 10, 10, 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]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438097642 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438097642 Building ZINC001438168028 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438168028 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/618 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)c(Cl)cc1I)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001438168028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438168028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 31 natoms 30 natoms 29 natoms 28 names: ZINC001438168028 none O=C(Nc1cc(F)c(Cl)cc1I)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'I', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 16, 1, 1, 18, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 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] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 39, 39, 6, 6, 6, 6] 45 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/619 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/619' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)c(Cl)cc1I)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001438168028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438168028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 31 natoms 30 natoms 29 natoms 28 names: ZINC001438168028 none O=C(Nc1cc(F)c(Cl)cc1I)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'I', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 16, 1, 1, 18, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 6, 6, 1, 6, 6, 6, 11, 37, 37, 6, 6, 6, 6] 44 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438168028 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028 Building ZINC001438168028 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438168028 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 618) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cc(F)c(Cl)cc1I)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001438168028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438168028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 31 natoms 30 natoms 29 natoms 28 names: ZINC001438168028 none O=C(Nc1cc(F)c(Cl)cc1I)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'I', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 16, 1, 1, 18, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 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] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 39, 39, 6, 6, 6, 6] 45 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 619) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cc(F)c(Cl)cc1I)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001438168028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438168028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 31 natoms 30 natoms 29 natoms 28 names: ZINC001438168028 none O=C(Nc1cc(F)c(Cl)cc1I)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'I', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 16, 1, 1, 18, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 6, 6, 1, 6, 6, 6, 11, 37, 37, 6, 6, 6, 6] 44 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438168028 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438168028 Building ZINC001438178238 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438178238 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/620 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCN1c2ccccc2Sc2ccccc21)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001438178238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438178238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001438178238 none CN(CCCN1c2ccccc2Sc2ccccc21)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 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, 7] 0 hydrogens 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, 12, 17, 19, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 29, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 5, 5, 5, 12, 12, 18, 18, 19, 19, 30, 30, 30, 30, 30, 30, 30, 30, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4] 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, 59]) total number of confs: 127 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/621 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/621' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCN1c2ccccc2Sc2ccccc21)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001438178238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438178238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001438178238 none CN(CCCN1c2ccccc2Sc2ccccc21)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 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, 7] 0 hydrogens 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, 12, 17, 19, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 30, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 5, 5, 5, 5, 12, 12, 18, 18, 19, 19, 31, 31, 31, 31, 31, 31, 31, 31, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 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, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 124 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438178238 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238 Building ZINC001438178238 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438178238 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 620) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(CCCN1c2ccccc2Sc2ccccc21)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001438178238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438178238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001438178238 none CN(CCCN1c2ccccc2Sc2ccccc21)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 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, 7] 0 hydrogens 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, 12, 17, 19, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 29, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 5, 5, 5, 12, 12, 18, 18, 19, 19, 30, 30, 30, 30, 30, 30, 30, 30, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4] 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, 59]) total number of confs: 127 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 621) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(CCCN1c2ccccc2Sc2ccccc21)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001438178238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438178238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001438178238 none CN(CCCN1c2ccccc2Sc2ccccc21)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 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, 7] 0 hydrogens 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, 12, 17, 19, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 30, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 5, 5, 5, 5, 12, 12, 18, 18, 19, 19, 31, 31, 31, 31, 31, 31, 31, 31, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 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, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 124 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438178238 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438178238 Building ZINC001438208483 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438208483 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/622 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)cc(Cl)c1) `ZINC001438208483.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438208483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001438208483 none COCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 10, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 14, 14, 14, 6, 14, 14, 14, 24, 24, 24, 16, 16, 10, 10, 6, 6, 14, 6, 14] 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]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/623 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/623' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)cc(Cl)c1) `ZINC001438208483.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438208483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001438208483 none COCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 17, 11, 7, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 7, 15, 15, 15, 7, 15, 15, 15, 25, 25, 25, 17, 17, 11, 11, 5, 5, 15, 7, 15] 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]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438208483 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483 Building ZINC001438208483 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438208483 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 622) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)cc(Cl)c1) `ZINC001438208483.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438208483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001438208483 none COCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 10, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 14, 14, 14, 6, 14, 14, 14, 24, 24, 24, 16, 16, 10, 10, 6, 6, 14, 6, 14] 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]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 623) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)cc(Cl)c1) `ZINC001438208483.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438208483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001438208483 none COCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 17, 11, 7, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 7, 15, 15, 15, 7, 15, 15, 15, 25, 25, 25, 17, 17, 11, 11, 5, 5, 15, 7, 15] 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]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438208483 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438208483 Building ZINC001438316430 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438316430 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/624 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1c2ccccc2C[C@@H]1Cc1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001438316430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438316430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001438316430 none O=C(N1c2ccccc2C[C@@H]1Cc1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 26, 26, 26, 26, 26, 1, 1, 1, 11, 11, 11, 11, 11, 8, 8, 8, 8, 8, 8, 21, 21, 26, 26, 26, 26, 26, 11, 11] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/625 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/625' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1c2ccccc2C[C@@H]1Cc1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001438316430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438316430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001438316430 none O=C(N1c2ccccc2C[C@@H]1Cc1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 19, 23, 23, 21, 23, 23, 1, 1, 1, 10, 10, 10, 10, 10, 8, 8, 8, 8, 8, 8, 19, 19, 23, 23, 19, 23, 23, 10, 10] 47 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438316430 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430 Building ZINC001438316430 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438316430 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 624) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(N1c2ccccc2C[C@@H]1Cc1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001438316430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438316430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001438316430 none O=C(N1c2ccccc2C[C@@H]1Cc1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 26, 26, 26, 26, 26, 1, 1, 1, 11, 11, 11, 11, 11, 8, 8, 8, 8, 8, 8, 21, 21, 26, 26, 26, 26, 26, 11, 11] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 625) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/625: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(N1c2ccccc2C[C@@H]1Cc1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001438316430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438316430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001438316430 none O=C(N1c2ccccc2C[C@@H]1Cc1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 19, 23, 23, 21, 23, 23, 1, 1, 1, 10, 10, 10, 10, 10, 8, 8, 8, 8, 8, 8, 19, 19, 23, 23, 19, 23, 23, 10, 10] 47 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438316430 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316430 Building ZINC001438316431 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438316431 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/626 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1c2ccccc2C[C@H]1Cc1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001438316431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438316431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001438316431 none O=C(N1c2ccccc2C[C@H]1Cc1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 21, 21, 17, 21, 21, 1, 1, 1, 10, 10, 10, 10, 10, 6, 6, 6, 6, 6, 6, 17, 17, 21, 21, 17, 21, 21, 10, 10] 44 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/627 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/627' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1c2ccccc2C[C@H]1Cc1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001438316431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438316431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001438316431 none O=C(N1c2ccccc2C[C@H]1Cc1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 19, 25, 25, 19, 25, 25, 1, 1, 1, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7, 7, 19, 19, 25, 25, 19, 25, 25, 12, 12] 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]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438316431 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431 Building ZINC001438316431 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438316431 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 626) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1c2ccccc2C[C@H]1Cc1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001438316431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438316431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001438316431 none O=C(N1c2ccccc2C[C@H]1Cc1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 21, 21, 17, 21, 21, 1, 1, 1, 10, 10, 10, 10, 10, 6, 6, 6, 6, 6, 6, 17, 17, 21, 21, 17, 21, 21, 10, 10] 44 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 627) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1c2ccccc2C[C@H]1Cc1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001438316431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438316431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001438316431 none O=C(N1c2ccccc2C[C@H]1Cc1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 19, 25, 25, 19, 25, 25, 1, 1, 1, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7, 7, 19, 19, 25, 25, 19, 25, 25, 12, 12] 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]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438316431 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438316431 Building ZINC001438384977 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438384977 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/628 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(n2nc3c(c2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCC3)cc1) `ZINC001438384977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438384977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001438384977 none Cc1ccc(n2nc3c(c2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 24, 24, 24, 12, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 24, 24, 24, 24, 29, 29, 29, 29, 29, 29, 29, 12, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 29, 29] 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]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/629 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/629' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(n2nc3c(c2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCC3)cc1) `ZINC001438384977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438384977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001438384977 none Cc1ccc(n2nc3c(c2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 23, 11, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 23, 23, 23, 23, 28, 28, 28, 28, 28, 28, 28, 11, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 28, 28] 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]) total number of confs: 68 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438384977 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977 Building ZINC001438384977 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438384977 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 628) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/628: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(n2nc3c(c2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCC3)cc1) `ZINC001438384977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438384977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001438384977 none Cc1ccc(n2nc3c(c2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 24, 24, 24, 12, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 24, 24, 24, 24, 29, 29, 29, 29, 29, 29, 29, 12, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 29, 29] 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]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 629) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/629: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(n2nc3c(c2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCC3)cc1) `ZINC001438384977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438384977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001438384977 none Cc1ccc(n2nc3c(c2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 23, 11, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 23, 23, 23, 23, 28, 28, 28, 28, 28, 28, 28, 11, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 28, 28] 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]) total number of confs: 68 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438384977 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438384977 Building ZINC001438463492 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438463492 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/630 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccncc1) `ZINC001438463492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438463492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001438463492 none CCCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccncc1 NO_LONG_NAME dock atom types: ['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', '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', 'H', 'H', 'H'] dock atom type numbers: [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, 1, 1, 1, 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, 7] dock color type numbers: [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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 3, 6, 6, 5, 6, 6, 11, 11, 11, 11, 11, 8, 8, 7, 7, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 6, 6, 6, 6] 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]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/631 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/631' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccncc1) `ZINC001438463492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438463492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001438463492 none CCCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccncc1 NO_LONG_NAME dock atom types: ['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', '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', 'H', 'H', 'H'] dock atom type numbers: [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, 1, 1, 1, 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, 7] dock color type numbers: [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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 3, 6, 6, 3, 6, 6, 11, 11, 11, 11, 11, 8, 8, 7, 7, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 6, 6, 6, 6] 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]) total number of confs: 91 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438463492 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492 Building ZINC001438463492 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438463492 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 630) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccncc1) `ZINC001438463492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438463492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001438463492 none CCCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccncc1 NO_LONG_NAME dock atom types: ['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', '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', 'H', 'H', 'H'] dock atom type numbers: [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, 1, 1, 1, 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, 7] dock color type numbers: [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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 3, 6, 6, 5, 6, 6, 11, 11, 11, 11, 11, 8, 8, 7, 7, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 6, 6, 6, 6] 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]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 631) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccncc1) `ZINC001438463492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438463492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001438463492 none CCCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccncc1 NO_LONG_NAME dock atom types: ['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', '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', 'H', 'H', 'H'] dock atom type numbers: [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, 1, 1, 1, 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, 7] dock color type numbers: [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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 3, 6, 6, 3, 6, 6, 11, 11, 11, 11, 11, 8, 8, 7, 7, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 6, 6, 6, 6] 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]) total number of confs: 91 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438463492 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438463492 Building ZINC001438572681 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438572681 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/632 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)[C@H](c2cccc(C(F)(F)F)c2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001438572681.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438572681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001438572681 none CC1(C)[C@H](c2cccc(C(F)(F)F)c2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 7, 7, 7, 7, 7, 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, 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: [7, 7, 7, 7, 7, 7, 20, 20, 7, 20, 20, 20, 20, 20, 20, 7, 7, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 7, 7, 7, 7, 7, 7, 20, 20, 14, 20, 7, 7, 7, 7, 6, 9, 9, 6, 9, 9, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/633 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/633' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)[C@H](c2cccc(C(F)(F)F)c2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001438572681.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438572681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001438572681 none CC1(C)[C@H](c2cccc(C(F)(F)F)c2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 7, 7, 7, 7, 7, 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, 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: [8, 8, 8, 8, 8, 8, 23, 23, 12, 23, 23, 23, 23, 23, 23, 8, 8, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 9, 9, 5, 9, 9, 5, 8, 8, 8, 8, 8, 8, 23, 23, 8, 23, 8, 8, 8, 8, 5, 9, 9, 9, 9, 9, 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]) total number of confs: 88 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438572681 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681 Building ZINC001438572681 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438572681 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 632) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC1(C)[C@H](c2cccc(C(F)(F)F)c2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001438572681.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438572681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001438572681 none CC1(C)[C@H](c2cccc(C(F)(F)F)c2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 7, 7, 7, 7, 7, 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, 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: [7, 7, 7, 7, 7, 7, 20, 20, 7, 20, 20, 20, 20, 20, 20, 7, 7, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 7, 7, 7, 7, 7, 7, 20, 20, 14, 20, 7, 7, 7, 7, 6, 9, 9, 6, 9, 9, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 633) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC1(C)[C@H](c2cccc(C(F)(F)F)c2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001438572681.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438572681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001438572681 none CC1(C)[C@H](c2cccc(C(F)(F)F)c2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 7, 7, 7, 7, 7, 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, 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: [8, 8, 8, 8, 8, 8, 23, 23, 12, 23, 23, 23, 23, 23, 23, 8, 8, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 9, 9, 5, 9, 9, 5, 8, 8, 8, 8, 8, 8, 23, 23, 8, 23, 8, 8, 8, 8, 5, 9, 9, 9, 9, 9, 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]) total number of confs: 88 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438572681 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572681 Building ZINC001438572687 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438572687 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/634 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)[C@@H](c2cccc(C(F)(F)F)c2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001438572687.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438572687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001438572687 none CC1(C)[C@@H](c2cccc(C(F)(F)F)c2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 7, 7, 7, 7, 7, 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, 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: [8, 8, 8, 8, 8, 8, 23, 23, 8, 23, 23, 23, 23, 23, 23, 8, 8, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 10, 10, 10, 10, 10, 5, 8, 8, 8, 8, 8, 8, 23, 23, 8, 23, 8, 8, 8, 8, 5, 10, 10, 10, 10, 10, 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/635 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/635' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)[C@@H](c2cccc(C(F)(F)F)c2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001438572687.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438572687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001438572687 none CC1(C)[C@@H](c2cccc(C(F)(F)F)c2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 7, 7, 7, 7, 7, 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, 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: [7, 7, 7, 7, 7, 7, 19, 19, 7, 19, 19, 19, 19, 19, 19, 7, 7, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 7, 7, 7, 7, 7, 7, 19, 19, 7, 19, 7, 7, 7, 7, 6, 9, 9, 9, 9, 9, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438572687 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687 Building ZINC001438572687 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438572687 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 634) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC1(C)[C@@H](c2cccc(C(F)(F)F)c2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001438572687.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438572687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001438572687 none CC1(C)[C@@H](c2cccc(C(F)(F)F)c2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 7, 7, 7, 7, 7, 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, 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: [8, 8, 8, 8, 8, 8, 23, 23, 8, 23, 23, 23, 23, 23, 23, 8, 8, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 10, 10, 10, 10, 10, 5, 8, 8, 8, 8, 8, 8, 23, 23, 8, 23, 8, 8, 8, 8, 5, 10, 10, 10, 10, 10, 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 635) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC1(C)[C@@H](c2cccc(C(F)(F)F)c2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001438572687.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438572687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001438572687 none CC1(C)[C@@H](c2cccc(C(F)(F)F)c2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 7, 7, 7, 7, 7, 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, 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: [7, 7, 7, 7, 7, 7, 19, 19, 7, 19, 19, 19, 19, 19, 19, 7, 7, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 7, 7, 7, 7, 7, 7, 19, 19, 7, 19, 7, 7, 7, 7, 6, 9, 9, 9, 9, 9, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438572687 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438572687 Building ZINC001438619369 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438619369 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/636 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(Cc2ccc(F)c(F)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001438619369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438619369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001438619369 none C[C@]1(Cc2ccc(F)c(F)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 19, 32, 32, 32, 32, 32, 32, 32, 11, 11, 11, 5, 2, 6, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 19, 19, 32, 32, 32, 11, 11, 11, 11, 11, 11, 6, 6] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/637 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/637' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(Cc2ccc(F)c(F)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001438619369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438619369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001438619369 none C[C@]1(Cc2ccc(F)c(F)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 18, 31, 31, 31, 31, 31, 31, 31, 13, 13, 13, 6, 2, 9, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 13, 18, 18, 31, 31, 31, 13, 13, 13, 13, 13, 13, 8, 8] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438619369 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369 Building ZINC001438619369 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438619369 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 636) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@]1(Cc2ccc(F)c(F)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001438619369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438619369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001438619369 none C[C@]1(Cc2ccc(F)c(F)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 19, 32, 32, 32, 32, 32, 32, 32, 11, 11, 11, 5, 2, 6, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 19, 19, 32, 32, 32, 11, 11, 11, 11, 11, 11, 6, 6] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 637) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@]1(Cc2ccc(F)c(F)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001438619369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438619369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001438619369 none C[C@]1(Cc2ccc(F)c(F)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 18, 31, 31, 31, 31, 31, 31, 31, 13, 13, 13, 6, 2, 9, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 13, 18, 18, 31, 31, 31, 13, 13, 13, 13, 13, 13, 8, 8] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438619369 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619369 Building ZINC001438619373 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438619373 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/638 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(Cc2ccc(F)c(F)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001438619373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438619373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001438619373 none C[C@@]1(Cc2ccc(F)c(F)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 17, 30, 30, 30, 30, 30, 30, 30, 13, 13, 13, 6, 2, 9, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 13, 17, 17, 30, 30, 30, 13, 13, 13, 13, 13, 13, 8, 8] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/639 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/639' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(Cc2ccc(F)c(F)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001438619373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438619373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001438619373 none C[C@@]1(Cc2ccc(F)c(F)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 19, 32, 32, 32, 32, 32, 32, 32, 11, 11, 11, 5, 2, 6, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 19, 19, 32, 32, 32, 11, 11, 11, 11, 11, 11, 6, 6] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438619373 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373 Building ZINC001438619373 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438619373 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 638) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@]1(Cc2ccc(F)c(F)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001438619373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438619373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001438619373 none C[C@@]1(Cc2ccc(F)c(F)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 17, 30, 30, 30, 30, 30, 30, 30, 13, 13, 13, 6, 2, 9, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 13, 17, 17, 30, 30, 30, 13, 13, 13, 13, 13, 13, 8, 8] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 639) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@]1(Cc2ccc(F)c(F)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001438619373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438619373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001438619373 none C[C@@]1(Cc2ccc(F)c(F)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 19, 32, 32, 32, 32, 32, 32, 32, 11, 11, 11, 5, 2, 6, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 19, 19, 32, 32, 32, 11, 11, 11, 11, 11, 11, 6, 6] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438619373 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438619373 Building ZINC001438694035 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438694035 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/640 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2nc3ccccc3[nH]2)C2CCCCC2)cc1Cl) `ZINC001438694035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438694035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001438694035 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2nc3ccccc3[nH]2)C2CCCCC2)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 15, 15, 15, 15, 15, 6, 6, 6, 11, 11, 11, 6, 6, 3, 13, 13, 13, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/641 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/641' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2nc3ccccc3[nH]2)C2CCCCC2)cc1Cl) `ZINC001438694035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438694035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001438694035 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2nc3ccccc3[nH]2)C2CCCCC2)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 4, 4, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 15, 15, 15, 15, 15, 6, 6, 6, 10, 10, 10, 6, 6, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438694035 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035 Building ZINC001438694035 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438694035 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 640) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2nc3ccccc3[nH]2)C2CCCCC2)cc1Cl) `ZINC001438694035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438694035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001438694035 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2nc3ccccc3[nH]2)C2CCCCC2)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 15, 15, 15, 15, 15, 6, 6, 6, 11, 11, 11, 6, 6, 3, 13, 13, 13, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 641) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2nc3ccccc3[nH]2)C2CCCCC2)cc1Cl) `ZINC001438694035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438694035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001438694035 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2nc3ccccc3[nH]2)C2CCCCC2)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 4, 4, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 15, 15, 15, 15, 15, 6, 6, 6, 10, 10, 10, 6, 6, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438694035 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694035 Building ZINC001438694039 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438694039 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/642 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2nc3ccccc3[nH]2)C2CCCCC2)cc1Cl) `ZINC001438694039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438694039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001438694039 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2nc3ccccc3[nH]2)C2CCCCC2)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 4, 4, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 14, 14, 14, 14, 14, 6, 6, 6, 10, 10, 10, 6, 6, 4, 15, 15, 15, 15, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 80 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/643 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/643' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2nc3ccccc3[nH]2)C2CCCCC2)cc1Cl) `ZINC001438694039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438694039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001438694039 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2nc3ccccc3[nH]2)C2CCCCC2)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 15, 15, 15, 15, 15, 6, 6, 6, 10, 10, 10, 6, 6, 3, 12, 12, 12, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 84 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438694039 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039 Building ZINC001438694039 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438694039 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 642) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2nc3ccccc3[nH]2)C2CCCCC2)cc1Cl) `ZINC001438694039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438694039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001438694039 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2nc3ccccc3[nH]2)C2CCCCC2)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 4, 4, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 14, 14, 14, 14, 14, 6, 6, 6, 10, 10, 10, 6, 6, 4, 15, 15, 15, 15, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 80 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 643) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2nc3ccccc3[nH]2)C2CCCCC2)cc1Cl) `ZINC001438694039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438694039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001438694039 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2nc3ccccc3[nH]2)C2CCCCC2)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 15, 15, 15, 15, 15, 6, 6, 6, 10, 10, 10, 6, 6, 3, 12, 12, 12, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 84 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438694039 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438694039 Building ZINC001438857137 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438857137 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/644 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/644' -> `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)NCC[C@@H]1CCCC1(F)F) `ZINC001438857137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438857137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001438857137 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCC1(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.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', 'C.3', 'C.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'] dock atom type 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, 5, 5, 5, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 12, 12, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/645 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/645' -> `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)NCC[C@@H]1CCCC1(F)F) `ZINC001438857137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438857137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001438857137 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCC1(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.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', 'C.3', 'C.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'] dock atom type 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, 5, 5, 5, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 11, 11, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 11, 11, 11, 11, 3, 3, 3, 2, 11, 11, 11, 11, 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438857137 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137 Building ZINC001438857137 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438857137 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 644) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCC1(F)F) `ZINC001438857137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438857137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001438857137 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCC1(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.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', 'C.3', 'C.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'] dock atom type 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, 5, 5, 5, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 12, 12, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 645) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCC1(F)F) `ZINC001438857137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438857137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001438857137 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCC1(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.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', 'C.3', 'C.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'] dock atom type 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, 5, 5, 5, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 11, 11, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 11, 11, 11, 11, 3, 3, 3, 2, 11, 11, 11, 11, 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438857137 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857137 Building ZINC001438857157 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438857157 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/646 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/646' -> `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)NCC[C@H]1CCCC1(F)F) `ZINC001438857157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438857157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001438857157 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCCC1(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.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', 'C.3', 'C.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'] dock atom type 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, 5, 5, 5, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 12, 12, 12, 12, 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/647 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/647' -> `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)NCC[C@H]1CCCC1(F)F) `ZINC001438857157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438857157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001438857157 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCCC1(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.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', 'C.3', 'C.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'] dock atom type 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, 5, 5, 5, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 14, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 10, 10, 13, 13, 17, 17, 17, 17, 17, 17] 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438857157 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157 Building ZINC001438857157 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438857157 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 646) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCCC1(F)F) `ZINC001438857157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438857157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001438857157 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCCC1(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.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', 'C.3', 'C.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'] dock atom type 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, 5, 5, 5, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 12, 12, 12, 12, 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 647) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCCC1(F)F) `ZINC001438857157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438857157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001438857157 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCCC1(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.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', 'C.3', 'C.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'] dock atom type 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, 5, 5, 5, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 14, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 10, 10, 13, 13, 17, 17, 17, 17, 17, 17] 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438857157 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438857157 Building ZINC001438868383 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438868383 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/648 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1cc(Cl)cc(Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001438868383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438868383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001438868383 none O=C(NCCc1cc(Cl)cc(Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 23, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 14, 14, 23, 23, 44, 44, 44, 3, 1, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/649 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/649' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1cc(Cl)cc(Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001438868383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438868383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001438868383 none O=C(NCCc1cc(Cl)cc(Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 24, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 14, 14, 24, 24, 44, 44, 44, 3, 1, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438868383 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383 Building ZINC001438868383 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438868383 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 648) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(NCCc1cc(Cl)cc(Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001438868383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438868383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001438868383 none O=C(NCCc1cc(Cl)cc(Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 23, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 14, 14, 23, 23, 44, 44, 44, 3, 1, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 649) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(NCCc1cc(Cl)cc(Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001438868383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438868383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001438868383 none O=C(NCCc1cc(Cl)cc(Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 24, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 14, 14, 24, 24, 44, 44, 44, 3, 1, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001438868383 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001438868383 Building ZINC001439085364 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439085364 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/650 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnc2ccccc2c1Br)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001439085364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439085364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC001439085364 none O=C(Nc1cnc2ccccc2c1Br)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens 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, 1, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 12, 12, 12, 12, 12, 8, 33, 33, 33, 33, 33, 12, 12] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/651 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/651' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnc2ccccc2c1Br)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001439085364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439085364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC001439085364 none O=C(Nc1cnc2ccccc2c1Br)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens 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, 1, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 12, 12, 12, 12, 12, 8, 33, 33, 33, 33, 33, 12, 12] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439085364 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364 Building ZINC001439085364 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439085364 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 650) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/650: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Nc1cnc2ccccc2c1Br)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001439085364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439085364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC001439085364 none O=C(Nc1cnc2ccccc2c1Br)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens 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, 1, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 12, 12, 12, 12, 12, 8, 33, 33, 33, 33, 33, 12, 12] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 651) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/651: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Nc1cnc2ccccc2c1Br)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001439085364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439085364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC001439085364 none O=C(Nc1cnc2ccccc2c1Br)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens 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, 1, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 12, 12, 12, 12, 12, 8, 33, 33, 33, 33, 33, 12, 12] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439085364 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439085364 Building ZINC001439180846 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439180846 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/652 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cc(I)cc(C(F)(F)F)c2C)c1) `ZINC001439180846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439180846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001439180846 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cc(I)cc(C(F)(F)F)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'I', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 18, 1, 1, 5, 15, 15, 15, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 1, 11, 11, 1, 1, 1, 1, 6, 6, 6, 21, 21, 21, 9, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 1, 11, 11, 6, 21, 14, 21, 21, 21, 11] 50 rigid atoms, others: [5, 6, 7, 8] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/653 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/653' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cc(I)cc(C(F)(F)F)c2C)c1) `ZINC001439180846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439180846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001439180846 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cc(I)cc(C(F)(F)F)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'I', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 18, 1, 1, 5, 15, 15, 15, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 1, 1, 1, 1, 5, 5, 5, 20, 20, 20, 9, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 11, 11, 11, 5, 20, 13, 20, 20, 20, 11] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439180846 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846 Building ZINC001439180846 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439180846 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 652) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cc(I)cc(C(F)(F)F)c2C)c1) `ZINC001439180846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439180846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001439180846 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cc(I)cc(C(F)(F)F)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'I', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 18, 1, 1, 5, 15, 15, 15, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 1, 11, 11, 1, 1, 1, 1, 6, 6, 6, 21, 21, 21, 9, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 1, 11, 11, 6, 21, 14, 21, 21, 21, 11] 50 rigid atoms, others: [5, 6, 7, 8] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 653) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cc(I)cc(C(F)(F)F)c2C)c1) `ZINC001439180846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439180846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001439180846 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cc(I)cc(C(F)(F)F)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'I', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 18, 1, 1, 5, 15, 15, 15, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 1, 1, 1, 1, 5, 5, 5, 20, 20, 20, 9, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 11, 11, 11, 5, 20, 13, 20, 20, 20, 11] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439180846 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439180846 Building ZINC001439185040 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439185040 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/654 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCOc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001439185040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439185040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001439185040 none O=C(N[C@H]1CCOc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens 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, 1, 8, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 8, 29, 29, 29, 29, 29, 29, 29, 6, 1, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/655 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/655' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCOc2ccc(Br)cc21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001439185040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439185040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001439185040 none O=C(N[C@H]1CCOc2ccc(Br)cc21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens 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, 1, 8, 8, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 8, 31, 31, 31, 31, 31, 31, 31, 6, 1, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439185040 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040 Building ZINC001439185040 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439185040 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 654) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@H]1CCOc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001439185040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439185040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001439185040 none O=C(N[C@H]1CCOc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens 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, 1, 8, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 8, 29, 29, 29, 29, 29, 29, 29, 6, 1, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 655) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@H]1CCOc2ccc(Br)cc21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001439185040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439185040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001439185040 none O=C(N[C@H]1CCOc2ccc(Br)cc21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens 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, 1, 8, 8, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 8, 31, 31, 31, 31, 31, 31, 31, 6, 1, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439185040 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439185040 Building ZINC001439353656 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439353656 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/656 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)Cc2ccc(Cl)cc2Oc2ccc(Cl)cc2)cn1) `ZINC001439353656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439353656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001439353656 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)Cc2ccc(Cl)cc2Oc2ccc(Cl)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 8, 13, 13, 11, 13, 13, 13, 13, 23, 27, 27, 23, 23, 27, 27, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 4, 8, 8, 13, 13, 13, 27, 27, 27, 27, 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: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/657 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/657' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)Cc2ccc(Cl)cc2Oc2ccc(Cl)cc2)cn1) `ZINC001439353656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439353656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001439353656 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)Cc2ccc(Cl)cc2Oc2ccc(Cl)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 8, 13, 13, 13, 13, 13, 13, 13, 23, 27, 27, 23, 23, 27, 27, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 4, 8, 8, 13, 13, 13, 27, 27, 27, 27, 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: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439353656 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656 Building ZINC001439353656 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439353656 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 656) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)Cc2ccc(Cl)cc2Oc2ccc(Cl)cc2)cn1) `ZINC001439353656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439353656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001439353656 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)Cc2ccc(Cl)cc2Oc2ccc(Cl)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 8, 13, 13, 11, 13, 13, 13, 13, 23, 27, 27, 23, 23, 27, 27, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 4, 8, 8, 13, 13, 13, 27, 27, 27, 27, 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: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 657) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)Cc2ccc(Cl)cc2Oc2ccc(Cl)cc2)cn1) `ZINC001439353656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439353656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001439353656 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)Cc2ccc(Cl)cc2Oc2ccc(Cl)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 8, 13, 13, 13, 13, 13, 13, 13, 23, 27, 27, 23, 23, 27, 27, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 4, 8, 8, 13, 13, 13, 27, 27, 27, 27, 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: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439353656 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439353656 Building ZINC001439522294 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439522294 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/658 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(OCCC3CCCCC3)c2)cn1) `ZINC001439522294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439522294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001439522294 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(OCCC3CCCCC3)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', 'Br', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 12, 5, 5, 5, 5, 5, 5, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 12, 15, 25, 37, 37, 37, 37, 37, 4, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 4, 15, 15, 25, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 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: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/659 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/659' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(OCCC3CCCCC3)c2)cn1) `ZINC001439522294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439522294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001439522294 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(OCCC3CCCCC3)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', 'Br', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 12, 5, 5, 5, 5, 5, 5, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 13, 16, 28, 41, 41, 41, 41, 41, 4, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 4, 16, 16, 28, 28, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 4, 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: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439522294 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294 Building ZINC001439522294 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439522294 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 658) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(OCCC3CCCCC3)c2)cn1) `ZINC001439522294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439522294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001439522294 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(OCCC3CCCCC3)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', 'Br', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 12, 5, 5, 5, 5, 5, 5, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 12, 15, 25, 37, 37, 37, 37, 37, 4, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 4, 15, 15, 25, 25, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 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: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 659) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(OCCC3CCCCC3)c2)cn1) `ZINC001439522294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439522294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001439522294 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(OCCC3CCCCC3)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', 'Br', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 12, 5, 5, 5, 5, 5, 5, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 13, 16, 28, 41, 41, 41, 41, 41, 4, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 4, 16, 16, 28, 28, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 4, 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: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439522294 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439522294 Building ZINC001439615093 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439615093 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/660 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1c(Cl)cc(Br)cc1Cl)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001439615093.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439615093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001439615093 none O=C(NCc1c(Cl)cc(Br)cc1Cl)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 16, 1, 1, 17, 1, 1, 16, 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] dock color type numbers: [6, 9, 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] 0 hydrogens 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, 19, 26, 26, 26, 21, 19, 26, 26, 26, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 5, 19, 19, 26, 26, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/661 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/661' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1c(Cl)cc(Br)cc1Cl)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001439615093.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439615093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001439615093 none O=C(NCc1c(Cl)cc(Br)cc1Cl)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 16, 1, 1, 17, 1, 1, 16, 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] dock color type numbers: [6, 9, 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] 0 hydrogens 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, 19, 26, 26, 26, 19, 19, 26, 26, 26, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 5, 19, 19, 26, 26, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439615093 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093 Building ZINC001439615093 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439615093 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 660) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1c(Cl)cc(Br)cc1Cl)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001439615093.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439615093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001439615093 none O=C(NCc1c(Cl)cc(Br)cc1Cl)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 16, 1, 1, 17, 1, 1, 16, 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] dock color type numbers: [6, 9, 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] 0 hydrogens 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, 19, 26, 26, 26, 21, 19, 26, 26, 26, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 5, 19, 19, 26, 26, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 661) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1c(Cl)cc(Br)cc1Cl)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001439615093.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439615093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001439615093 none O=C(NCc1c(Cl)cc(Br)cc1Cl)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 16, 1, 1, 17, 1, 1, 16, 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] dock color type numbers: [6, 9, 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] 0 hydrogens 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, 19, 26, 26, 26, 19, 19, 26, 26, 26, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 5, 19, 19, 26, 26, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439615093 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439615093 Building ZINC001439637502 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439637502 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/662 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)c2nc(c3ccccc3C)cs2)cn1) `ZINC001439637502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439637502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001439637502 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)c2nc(c3ccccc3C)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'S.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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 4, 4, 4, 20, 20, 8, 20, 20, 20, 4, 4, 2, 2, 5, 5, 5, 5, 5, 2, 1, 1, 2, 2, 2, 2, 2, 20, 20, 8, 20, 20, 20, 20, 4, 2] 50 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 17, 38, 37] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/663 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/663' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)c2nc(c3ccccc3C)cs2)cn1) `ZINC001439637502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439637502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001439637502 none CCn1cc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)c2nc(c3ccccc3C)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'S.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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 4, 4, 4, 20, 20, 6, 20, 20, 20, 4, 4, 2, 2, 6, 6, 6, 6, 6, 2, 1, 1, 2, 2, 2, 2, 2, 20, 20, 8, 20, 20, 20, 20, 4, 2] 50 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 17, 38, 37] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439637502 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502 Building ZINC001439637502 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439637502 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 662) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)N(Cc2ccccc2)c2nc(c3ccccc3C)cs2)cn1) `ZINC001439637502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439637502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001439637502 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)c2nc(c3ccccc3C)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'S.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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 4, 4, 4, 20, 20, 8, 20, 20, 20, 4, 4, 2, 2, 5, 5, 5, 5, 5, 2, 1, 1, 2, 2, 2, 2, 2, 20, 20, 8, 20, 20, 20, 20, 4, 2] 50 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 17, 38, 37] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 663) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)N(Cc2ccccc2)c2nc(c3ccccc3C)cs2)cn1) `ZINC001439637502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439637502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001439637502 none CCn1cc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)c2nc(c3ccccc3C)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'S.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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 4, 4, 4, 20, 20, 6, 20, 20, 20, 4, 4, 2, 2, 6, 6, 6, 6, 6, 2, 1, 1, 2, 2, 2, 2, 2, 20, 20, 8, 20, 20, 20, 20, 4, 2] 50 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 17, 38, 37] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439637502 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439637502 Building ZINC001439909576 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439909576 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/664 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/664' -> `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)cc2ccccc21) `ZINC001439909576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439909576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001439909576 none COc1cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc2ccccc21 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', '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, 5, 7, 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, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 22, 22, 22, 22, 22, 22, 22, 32, 32, 32, 22, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 22, 22, 22, 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]) total number of confs: 64 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/665 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/665' -> `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)cc2ccccc21) `ZINC001439909576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439909576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001439909576 none COc1cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc2ccccc21 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', '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, 5, 7, 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, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 17, 17, 17, 17, 17, 17, 17, 31, 31, 31, 17, 3, 3, 3, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 17, 17, 17, 17, 17] 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]) total number of confs: 62 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439909576 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576 Building ZINC001439909576 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439909576 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 664) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc2ccccc21) `ZINC001439909576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439909576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001439909576 none COc1cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc2ccccc21 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', '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, 5, 7, 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, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 22, 22, 22, 22, 22, 22, 22, 32, 32, 32, 22, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 22, 22, 22, 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]) total number of confs: 64 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 665) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc2ccccc21) `ZINC001439909576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439909576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001439909576 none COc1cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc2ccccc21 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', '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, 5, 7, 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, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 17, 17, 17, 17, 17, 17, 17, 31, 31, 31, 17, 3, 3, 3, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 17, 17, 17, 17, 17] 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]) total number of confs: 62 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439909576 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909576 Building ZINC001439909577 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439909577 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/666 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/666' -> `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)cc2ccccc21) `ZINC001439909577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439909577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001439909577 none COc1cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc2ccccc21 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', '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, 5, 7, 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, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 17, 17, 17, 17, 17, 17, 17, 32, 32, 32, 17, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 17, 17, 17, 17, 17] 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]) total number of confs: 70 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/667 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/667' -> `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)cc2ccccc21) `ZINC001439909577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439909577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001439909577 none COc1cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc2ccccc21 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', '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, 5, 7, 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, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 19, 19, 19, 19, 19, 19, 19, 28, 28, 28, 19, 4, 4, 4, 2, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 19, 19, 19, 19, 19] 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]) total number of confs: 76 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439909577 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577 Building ZINC001439909577 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439909577 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 666) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc2ccccc21) `ZINC001439909577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439909577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001439909577 none COc1cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc2ccccc21 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', '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, 5, 7, 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, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 17, 17, 17, 17, 17, 17, 17, 32, 32, 32, 17, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 17, 17, 17, 17, 17] 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]) total number of confs: 70 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 667) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc2ccccc21) `ZINC001439909577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439909577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001439909577 none COc1cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc2ccccc21 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', '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, 5, 7, 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, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 19, 19, 19, 19, 19, 19, 19, 28, 28, 28, 19, 4, 4, 4, 2, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 19, 19, 19, 19, 19] 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]) total number of confs: 76 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439909577 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439909577 Building ZINC001439926673 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439926673 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/668 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(=O)n(Cc2ccc(Cl)cc2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001439926673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439926673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001439926673 none O=C(Nc1ccc(=O)n(Cc2ccc(Cl)cc2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 16, 16, 16, 16, 16, 16, 37, 41, 41, 37, 37, 41, 41, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 16, 16, 37, 37, 41, 41, 41, 41, 16, 3, 1, 3] 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/669 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/669' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(=O)n(Cc2ccc(Cl)cc2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001439926673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439926673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001439926673 none O=C(Nc1ccc(=O)n(Cc2ccc(Cl)cc2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 16, 16, 16, 16, 16, 16, 37, 41, 41, 37, 39, 41, 41, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 16, 16, 37, 37, 41, 41, 41, 41, 16, 3, 1, 3] 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439926673 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673 Building ZINC001439926673 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439926673 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 668) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(=O)n(Cc2ccc(Cl)cc2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001439926673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439926673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001439926673 none O=C(Nc1ccc(=O)n(Cc2ccc(Cl)cc2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 16, 16, 16, 16, 16, 16, 37, 41, 41, 37, 37, 41, 41, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 16, 16, 37, 37, 41, 41, 41, 41, 16, 3, 1, 3] 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 669) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(=O)n(Cc2ccc(Cl)cc2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001439926673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439926673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001439926673 none O=C(Nc1ccc(=O)n(Cc2ccc(Cl)cc2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 16, 16, 16, 16, 16, 16, 37, 41, 41, 37, 39, 41, 41, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 16, 16, 37, 37, 41, 41, 41, 41, 16, 3, 1, 3] 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439926673 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439926673 Building ZINC001439959302 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439959302 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/670 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3c(cc(F)cc3Br)s2)cc1Cl) `ZINC001439959302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439959302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001439959302 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3c(cc(F)cc3Br)s2)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'S.3', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 1, 1, 15, 1, 1, 17, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 2, 10, 10, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21, 10, 10, 6, 10, 10, 10] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/671 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/671' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3c(cc(F)cc3Br)s2)cc1Cl) `ZINC001439959302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439959302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001439959302 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3c(cc(F)cc3Br)s2)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'S.3', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 1, 1, 15, 1, 1, 17, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 10, 10, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21, 10, 10, 6, 10, 10, 10] 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439959302 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302 Building ZINC001439959302 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439959302 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 670) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3c(cc(F)cc3Br)s2)cc1Cl) `ZINC001439959302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439959302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001439959302 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3c(cc(F)cc3Br)s2)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'S.3', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 1, 1, 15, 1, 1, 17, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 2, 10, 10, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21, 10, 10, 6, 10, 10, 10] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 671) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3c(cc(F)cc3Br)s2)cc1Cl) `ZINC001439959302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439959302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001439959302 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3c(cc(F)cc3Br)s2)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'S.3', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 1, 1, 15, 1, 1, 17, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 10, 10, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21, 10, 10, 6, 10, 10, 10] 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439959302 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439959302 Building ZINC001439975657 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439975657 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/672 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/672' -> `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)NCc1ccccc1SC(F)(F)F) `ZINC001439975657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439975657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001439975657 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1SC(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', 'S.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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 19, 19, 17, 19, 19, 19, 49, 49, 49, 49, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 3, 10, 10, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/673 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/673' -> `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)NCc1ccccc1SC(F)(F)F) `ZINC001439975657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439975657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001439975657 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1SC(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', 'S.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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 23, 23, 23, 23, 23, 23, 50, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 12, 12, 23, 23, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439975657 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657 Building ZINC001439975657 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439975657 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 672) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NCc1ccccc1SC(F)(F)F) `ZINC001439975657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439975657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001439975657 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1SC(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', 'S.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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 19, 19, 17, 19, 19, 19, 49, 49, 49, 49, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 3, 10, 10, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 673) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NCc1ccccc1SC(F)(F)F) `ZINC001439975657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439975657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001439975657 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1SC(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', 'S.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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 23, 23, 23, 23, 23, 23, 50, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 12, 12, 23, 23, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439975657 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439975657 Building ZINC001439996761 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439996761 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/674 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/674' -> `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)NC1(C2CCCCC2)CC1) `ZINC001439996761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439996761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001439996761 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1(C2CCCCC2)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', '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, 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] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 10, 10, 10, 10, 10, 6, 6, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 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, 54, 55, 56]) total number of confs: 65 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/675 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/675' -> `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)NC1(C2CCCCC2)CC1) `ZINC001439996761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439996761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001439996761 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1(C2CCCCC2)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', '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, 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] 0 hydrogens need rotated 50 conformations in 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, 3, 13, 13, 13, 13, 13, 13, 2, 2, 1, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 15, 15, 6, 6, 2, 2, 2, 13, 13, 5, 13, 2, 2, 2, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 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, 54, 55, 56]) total number of confs: 68 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439996761 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761 Building ZINC001439996761 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439996761 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 674) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1(C2CCCCC2)CC1) `ZINC001439996761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439996761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001439996761 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1(C2CCCCC2)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', '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, 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] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 10, 10, 10, 10, 10, 6, 6, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 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, 54, 55, 56]) total number of confs: 65 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 675) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1(C2CCCCC2)CC1) `ZINC001439996761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439996761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001439996761 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1(C2CCCCC2)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', '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, 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] 0 hydrogens need rotated 50 conformations in 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, 3, 13, 13, 13, 13, 13, 13, 2, 2, 1, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 15, 15, 6, 6, 2, 2, 2, 13, 13, 5, 13, 2, 2, 2, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 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, 54, 55, 56]) total number of confs: 68 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001439996761 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001439996761 Building ZINC001440175057 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440175057 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/676 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@H]1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)CC2) `ZINC001440175057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440175057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001440175057 none CC(C)(C)OC(=O)NC[C@@H]1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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: [45, 45, 45, 45, 43, 36, 43, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 45, 45, 45, 45, 45, 45, 45, 45, 45, 36, 17, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 8, 8, 8, 8] 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/677 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/677' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@H]1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)CC2) `ZINC001440175057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440175057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001440175057 none CC(C)(C)OC(=O)NC[C@@H]1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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: [42, 42, 42, 42, 41, 34, 41, 15, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 34, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001440175057 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057 Building ZINC001440175057 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440175057 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 676) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)OC(=O)NC[C@@H]1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)CC2) `ZINC001440175057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440175057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001440175057 none CC(C)(C)OC(=O)NC[C@@H]1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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: [45, 45, 45, 45, 43, 36, 43, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 45, 45, 45, 45, 45, 45, 45, 45, 45, 36, 17, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 8, 8, 8, 8] 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 677) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)OC(=O)NC[C@@H]1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)CC2) `ZINC001440175057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440175057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001440175057 none CC(C)(C)OC(=O)NC[C@@H]1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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: [42, 42, 42, 42, 41, 34, 41, 15, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 34, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001440175057 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175057 Building ZINC001440175064 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440175064 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/678 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H]1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)CC2) `ZINC001440175064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440175064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001440175064 none CC(C)(C)OC(=O)NC[C@H]1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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: [45, 45, 45, 45, 44, 35, 44, 16, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1, 9, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 45, 45, 45, 45, 45, 45, 45, 45, 45, 35, 16, 16, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 9, 9, 9, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/679 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/679' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H]1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)CC2) `ZINC001440175064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440175064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001440175064 none CC(C)(C)OC(=O)NC[C@H]1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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: [46, 46, 46, 46, 45, 36, 45, 18, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 46, 46, 46, 46, 46, 46, 46, 46, 46, 36, 18, 18, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 9, 9, 9, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001440175064 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064 Building ZINC001440175064 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440175064 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 678) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)OC(=O)NC[C@H]1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)CC2) `ZINC001440175064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440175064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001440175064 none CC(C)(C)OC(=O)NC[C@H]1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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: [45, 45, 45, 45, 44, 35, 44, 16, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1, 9, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 45, 45, 45, 45, 45, 45, 45, 45, 45, 35, 16, 16, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 9, 9, 9, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 679) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)OC(=O)NC[C@H]1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)CC2) `ZINC001440175064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440175064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001440175064 none CC(C)(C)OC(=O)NC[C@H]1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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: [46, 46, 46, 46, 45, 36, 45, 18, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 46, 46, 46, 46, 46, 46, 46, 46, 46, 36, 18, 18, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 9, 9, 9, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001440175064 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440175064 Building ZINC001440395275 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440395275 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/680 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](c2nc3ccccc3s2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001440395275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440395275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001440395275 none O=C(N1CCC[C@@H](c2nc3ccccc3s2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 1, 1, 14, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 31, 31, 31, 31, 31, 31, 31, 31, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 31, 31, 31, 31, 8, 8, 5, 5] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/681 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/681' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](c2nc3ccccc3s2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001440395275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440395275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001440395275 none O=C(N1CCC[C@@H](c2nc3ccccc3s2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 1, 1, 14, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 10, 10, 10, 10, 10, 10, 38, 38, 38, 38, 38, 38, 38, 38, 10, 1, 1, 1, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 38, 38, 38, 38, 10, 10, 5, 5] 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001440395275 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275 Building ZINC001440395275 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440395275 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 680) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCC[C@@H](c2nc3ccccc3s2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001440395275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440395275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001440395275 none O=C(N1CCC[C@@H](c2nc3ccccc3s2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 1, 1, 14, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 31, 31, 31, 31, 31, 31, 31, 31, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 31, 31, 31, 31, 8, 8, 5, 5] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 681) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCC[C@@H](c2nc3ccccc3s2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001440395275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440395275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001440395275 none O=C(N1CCC[C@@H](c2nc3ccccc3s2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 1, 1, 14, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 10, 10, 10, 10, 10, 10, 38, 38, 38, 38, 38, 38, 38, 38, 10, 1, 1, 1, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 38, 38, 38, 38, 10, 10, 5, 5] 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001440395275 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395275 Building ZINC001440395280 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440395280 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/682 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](c2nc3ccccc3s2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001440395280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440395280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001440395280 none O=C(N1CCC[C@H](c2nc3ccccc3s2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 1, 1, 14, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 10, 10, 10, 10, 10, 10, 39, 39, 39, 39, 39, 39, 39, 39, 10, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 39, 39, 39, 39, 10, 10, 4, 4] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/683 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/683' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](c2nc3ccccc3s2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001440395280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440395280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001440395280 none O=C(N1CCC[C@H](c2nc3ccccc3s2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 1, 1, 14, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 8, 8, 8, 8, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 8, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 32, 32, 32, 32, 8, 8, 4, 4] 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001440395280 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280 Building ZINC001440395280 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440395280 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 682) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCC[C@H](c2nc3ccccc3s2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001440395280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440395280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001440395280 none O=C(N1CCC[C@H](c2nc3ccccc3s2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 1, 1, 14, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 10, 10, 10, 10, 10, 10, 39, 39, 39, 39, 39, 39, 39, 39, 10, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 39, 39, 39, 39, 10, 10, 4, 4] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 683) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCC[C@H](c2nc3ccccc3s2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001440395280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440395280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001440395280 none O=C(N1CCC[C@H](c2nc3ccccc3s2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 1, 1, 14, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 8, 8, 8, 8, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 8, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 32, 32, 32, 32, 8, 8, 4, 4] 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001440395280 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440395280 Building ZINC001440864487 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001440864487 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/684 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001440864487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440864487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001440864487 none O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 24, 24, 24, 24, 24, 48, 50, 50, 48, 49, 50, 50, 24, 24, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 24, 24, 24, 24, 24, 24, 48, 48, 50, 50, 50, 50, 24, 24, 24, 24, 2, 1, 2] 50 rigid atoms, others: [1, 17, 18, 19] 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: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/685 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/685' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001440864487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440864487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001440864487 none O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 24, 24, 24, 24, 24, 48, 50, 50, 48, 49, 50, 50, 24, 24, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 24, 24, 24, 24, 24, 24, 48, 48, 50, 50, 50, 50, 24, 24, 24, 24, 2, 1, 2] 50 rigid atoms, others: [1, 17, 18, 19] 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: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/686 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/686' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001440864487.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001440864487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/2/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 49 natoms 48 natoms 47 natoms 46 names: ZINC001440864487 none O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 23, 23, 23, 23, 23, 47, 50, 50, 47, 49, 50, 50, 23, 23, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 23, 23, 23, 23, 23, 23, 47, 47, 50, 50, 50, 50, 23, 23, 23, 23, 2, 1, 2] 50 rigid atoms, others: [1, 17, 18, 19] 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: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/687 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/687' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001440864487.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001440864487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/3/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 49 natoms 48 natoms 47 natoms 46 names: ZINC001440864487 none O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 23, 23, 23, 23, 23, 47, 50, 50, 47, 49, 50, 50, 23, 23, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 23, 23, 23, 23, 23, 23, 47, 47, 50, 50, 50, 50, 23, 23, 23, 23, 2, 1, 2] 50 rigid atoms, others: [1, 17, 18, 19] 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: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001440864487 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 Building ZINC001440864487 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001440864487 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 684) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001440864487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440864487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001440864487 none O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 24, 24, 24, 24, 24, 48, 50, 50, 48, 49, 50, 50, 24, 24, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 24, 24, 24, 24, 24, 24, 48, 48, 50, 50, 50, 50, 24, 24, 24, 24, 2, 1, 2] 50 rigid atoms, others: [1, 17, 18, 19] 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: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 685) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001440864487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440864487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001440864487 none O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 24, 24, 24, 24, 24, 48, 50, 50, 48, 49, 50, 50, 24, 24, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 24, 24, 24, 24, 24, 24, 48, 48, 50, 50, 50, 50, 24, 24, 24, 24, 2, 1, 2] 50 rigid atoms, others: [1, 17, 18, 19] 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: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 686) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/686: 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(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001440864487.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001440864487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/2/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 49 natoms 48 natoms 47 natoms 46 names: ZINC001440864487 none O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 23, 23, 23, 23, 23, 47, 50, 50, 47, 49, 50, 50, 23, 23, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 23, 23, 23, 23, 23, 23, 47, 47, 50, 50, 50, 50, 23, 23, 23, 23, 2, 1, 2] 50 rigid atoms, others: [1, 17, 18, 19] 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: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 687) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/687: 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(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001440864487.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001440864487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/3/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 49 natoms 48 natoms 47 natoms 46 names: ZINC001440864487 none O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 23, 23, 23, 23, 23, 47, 50, 50, 47, 49, 50, 50, 23, 23, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 23, 23, 23, 23, 23, 23, 47, 47, 50, 50, 50, 50, 23, 23, 23, 23, 2, 1, 2] 50 rigid atoms, others: [1, 17, 18, 19] 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: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001440864487 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 Building ZINC001440864487 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001440864487 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 684) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001440864487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440864487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001440864487 none O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 24, 24, 24, 24, 24, 48, 50, 50, 48, 49, 50, 50, 24, 24, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 24, 24, 24, 24, 24, 24, 48, 48, 50, 50, 50, 50, 24, 24, 24, 24, 2, 1, 2] 50 rigid atoms, others: [1, 17, 18, 19] 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: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 685) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001440864487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440864487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001440864487 none O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 24, 24, 24, 24, 24, 48, 50, 50, 48, 49, 50, 50, 24, 24, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 24, 24, 24, 24, 24, 24, 48, 48, 50, 50, 50, 50, 24, 24, 24, 24, 2, 1, 2] 50 rigid atoms, others: [1, 17, 18, 19] 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: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 686) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/686: 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(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001440864487.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001440864487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/2/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 49 natoms 48 natoms 47 natoms 46 names: ZINC001440864487 none O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 23, 23, 23, 23, 23, 47, 50, 50, 47, 49, 50, 50, 23, 23, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 23, 23, 23, 23, 23, 23, 47, 47, 50, 50, 50, 50, 23, 23, 23, 23, 2, 1, 2] 50 rigid atoms, others: [1, 17, 18, 19] 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: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 687) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/687: 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(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001440864487.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001440864487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/3/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 49 natoms 48 natoms 47 natoms 46 names: ZINC001440864487 none O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 23, 23, 23, 23, 23, 47, 50, 50, 47, 49, 50, 50, 23, 23, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 23, 23, 23, 23, 23, 23, 47, 47, 50, 50, 50, 50, 23, 23, 23, 23, 2, 1, 2] 50 rigid atoms, others: [1, 17, 18, 19] 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: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001440864487 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 Building ZINC001440864487 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001440864487 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 684) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001440864487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440864487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001440864487 none O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 24, 24, 24, 24, 24, 48, 50, 50, 48, 49, 50, 50, 24, 24, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 24, 24, 24, 24, 24, 24, 48, 48, 50, 50, 50, 50, 24, 24, 24, 24, 2, 1, 2] 50 rigid atoms, others: [1, 17, 18, 19] 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: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 685) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001440864487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440864487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001440864487 none O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 24, 24, 24, 24, 24, 48, 50, 50, 48, 49, 50, 50, 24, 24, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 24, 24, 24, 24, 24, 24, 48, 48, 50, 50, 50, 50, 24, 24, 24, 24, 2, 1, 2] 50 rigid atoms, others: [1, 17, 18, 19] 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: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 686) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/686: 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(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001440864487.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001440864487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/2/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 49 natoms 48 natoms 47 natoms 46 names: ZINC001440864487 none O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 23, 23, 23, 23, 23, 47, 50, 50, 47, 49, 50, 50, 23, 23, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 23, 23, 23, 23, 23, 23, 47, 47, 50, 50, 50, 50, 23, 23, 23, 23, 2, 1, 2] 50 rigid atoms, others: [1, 17, 18, 19] 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: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 687) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/687: 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(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001440864487.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001440864487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/3/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 49 natoms 48 natoms 47 natoms 46 names: ZINC001440864487 none O=C(N1CCCN(Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 23, 23, 23, 23, 23, 47, 50, 50, 47, 49, 50, 50, 23, 23, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 23, 23, 23, 23, 23, 23, 47, 47, 50, 50, 50, 50, 23, 23, 23, 23, 2, 1, 2] 50 rigid atoms, others: [1, 17, 18, 19] 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: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001440864487 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001440864487 Building ZINC001441403672 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001441403672 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/688 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(S(=O)(=O)Nc2ccccc2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001441403672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001441403672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001441403672 none O=C(Nc1cccc(S(=O)(=O)Nc2ccccc2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 6, 6, 4, 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] 0 hydrogens need 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, 15, 2, 15, 15, 23, 23, 23, 47, 47, 47, 47, 47, 47, 15, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 15, 15, 2, 47, 47, 47, 47, 47, 47, 15, 3, 1, 3] 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]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/689 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/689' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(S(=O)(=O)Nc2ccccc2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001441403672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001441403672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001441403672 none O=C(Nc1cccc(S(=O)(=O)Nc2ccccc2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 6, 6, 4, 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] 0 hydrogens need 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, 15, 15, 15, 15, 23, 23, 23, 46, 46, 46, 46, 46, 46, 15, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 15, 15, 15, 46, 46, 46, 46, 46, 46, 15, 3, 1, 3] 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001441403672 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672 Building ZINC001441403672 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001441403672 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 688) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cccc(S(=O)(=O)Nc2ccccc2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001441403672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001441403672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001441403672 none O=C(Nc1cccc(S(=O)(=O)Nc2ccccc2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 6, 6, 4, 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] 0 hydrogens need 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, 15, 2, 15, 15, 23, 23, 23, 47, 47, 47, 47, 47, 47, 15, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 15, 15, 2, 47, 47, 47, 47, 47, 47, 15, 3, 1, 3] 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]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 689) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cccc(S(=O)(=O)Nc2ccccc2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001441403672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001441403672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001441403672 none O=C(Nc1cccc(S(=O)(=O)Nc2ccccc2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 6, 6, 4, 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] 0 hydrogens need 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, 15, 15, 15, 15, 23, 23, 23, 46, 46, 46, 46, 46, 46, 15, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 15, 15, 15, 46, 46, 46, 46, 46, 46, 15, 3, 1, 3] 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001441403672 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441403672 Building ZINC001441841747 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001441841747 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/690 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1)c1ccccc1) `ZINC001441841747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001441841747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001441841747 none CCN(C(=O)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 16, 27, 10, 5, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 16, 16, 10, 10, 3, 4, 4, 4, 4, 10, 10, 27, 27, 27, 27, 27] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/691 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1)c1ccccc1) `ZINC001441841747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001441841747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001441841747 none CCN(C(=O)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 26, 12, 26, 3, 3, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 25, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 12, 12, 10, 10, 3, 4, 4, 4, 4, 10, 10, 28, 28, 28, 28, 28] 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001441841747 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747 Building ZINC001441841747 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001441841747 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 690) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCN(C(=O)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1)c1ccccc1) `ZINC001441841747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001441841747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001441841747 none CCN(C(=O)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 16, 27, 10, 5, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 16, 16, 10, 10, 3, 4, 4, 4, 4, 10, 10, 27, 27, 27, 27, 27] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 691) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCN(C(=O)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1)c1ccccc1) `ZINC001441841747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001441841747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001441841747 none CCN(C(=O)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 26, 12, 26, 3, 3, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 25, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 12, 12, 10, 10, 3, 4, 4, 4, 4, 10, 10, 28, 28, 28, 28, 28] 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001441841747 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001441841747 Building ZINC001442225805 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442225805 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/692 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1sc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nc1c1ccc(Cl)cc1) `ZINC001442225805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442225805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001442225805 none Cc1sc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nc1c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.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'] dock atom type numbers: [5, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 35, 35, 34, 35, 35, 35, 33, 33, 33, 12, 12, 3, 4, 4, 4, 4, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/693 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/693' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1sc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nc1c1ccc(Cl)cc1) `ZINC001442225805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442225805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001442225805 none Cc1sc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nc1c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.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'] dock atom type numbers: [5, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 36, 36, 35, 35, 36, 36, 33, 33, 33, 12, 12, 3, 4, 4, 4, 4, 36, 36, 36, 36] 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001442225805 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805 Building ZINC001442225805 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442225805 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 692) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1sc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nc1c1ccc(Cl)cc1) `ZINC001442225805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442225805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001442225805 none Cc1sc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nc1c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.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'] dock atom type numbers: [5, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 35, 35, 34, 35, 35, 35, 33, 33, 33, 12, 12, 3, 4, 4, 4, 4, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 693) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1sc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nc1c1ccc(Cl)cc1) `ZINC001442225805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442225805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001442225805 none Cc1sc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nc1c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.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'] dock atom type numbers: [5, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 36, 36, 35, 35, 36, 36, 33, 33, 33, 12, 12, 3, 4, 4, 4, 4, 36, 36, 36, 36] 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001442225805 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442225805 Building ZINC001442313063 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442313063 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/694 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(C(F)(F)F)cc1) `ZINC001442313063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442313063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001442313063 none CCN(CC)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(C(F)(F)F)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 19, 17, 19, 33, 14, 17, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 19, 19, 17, 17, 19, 19, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 14, 14, 3, 5, 5, 5, 5, 19, 19, 19, 19] 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: 270 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/695 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/695' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(C(F)(F)F)cc1) `ZINC001442313063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442313063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001442313063 none CCN(CC)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(C(F)(F)F)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 14, 13, 14, 25, 9, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 14, 14, 13, 13, 14, 14, 14, 14, 14, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 9, 9, 3, 6, 6, 6, 6, 14, 14, 14, 14] 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: 205 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001442313063 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063 Building ZINC001442313063 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442313063 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 694) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCN(CC)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(C(F)(F)F)cc1) `ZINC001442313063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442313063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001442313063 none CCN(CC)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(C(F)(F)F)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 19, 17, 19, 33, 14, 17, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 19, 19, 17, 17, 19, 19, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 14, 14, 3, 5, 5, 5, 5, 19, 19, 19, 19] 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: 270 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 695) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCN(CC)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(C(F)(F)F)cc1) `ZINC001442313063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442313063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001442313063 none CCN(CC)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(C(F)(F)F)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 14, 13, 14, 25, 9, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 14, 14, 13, 13, 14, 14, 14, 14, 14, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 9, 9, 3, 6, 6, 6, 6, 14, 14, 14, 14] 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: 205 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001442313063 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313063 Building ZINC001442313068 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442313068 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/696 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(C(F)(F)F)cc1) `ZINC001442313068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442313068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001442313068 none CCN(CC)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(C(F)(F)F)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 14, 14, 14, 22, 10, 14, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 15, 15, 14, 15, 15, 15, 15, 15, 15, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 10, 3, 6, 6, 6, 6, 15, 15, 15, 15] 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: 167 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/697 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/697' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(C(F)(F)F)cc1) `ZINC001442313068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442313068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001442313068 none CCN(CC)[C@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(C(F)(F)F)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 18, 18, 18, 31, 14, 18, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 19, 19, 18, 19, 19, 19, 19, 19, 19, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 3, 5, 5, 5, 5, 19, 19, 19, 19] 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: 241 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001442313068 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068 Building ZINC001442313068 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442313068 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 696) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCN(CC)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(C(F)(F)F)cc1) `ZINC001442313068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442313068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001442313068 none CCN(CC)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(C(F)(F)F)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 14, 14, 14, 22, 10, 14, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 15, 15, 14, 15, 15, 15, 15, 15, 15, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 10, 3, 6, 6, 6, 6, 15, 15, 15, 15] 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: 167 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 697) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCN(CC)[C@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(C(F)(F)F)cc1) `ZINC001442313068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442313068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001442313068 none CCN(CC)[C@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(C(F)(F)F)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 18, 18, 18, 31, 14, 18, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 19, 19, 18, 19, 19, 19, 19, 19, 19, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 3, 5, 5, 5, 5, 19, 19, 19, 19] 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: 241 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001442313068 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442313068 Building ZINC001442465297 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442465297 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/698 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@H](C)c1cccc(C(F)(F)F)c1) `ZINC001442465297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442465297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001442465297 none COCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@H](C)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 6, 8, 10, 11, 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] 0 hydrogens 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, 7, 3, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 8, 8, 7, 7, 5, 5, 5, 5, 4, 4, 4, 12, 12, 12, 12] 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]) total number of confs: 61 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/699 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/699' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@H](C)c1cccc(C(F)(F)F)c1) `ZINC001442465297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442465297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001442465297 none COCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@H](C)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 6, 8, 10, 11, 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] 0 hydrogens 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, 10, 10, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 9, 9, 9, 26, 26, 17, 26, 26, 26, 26, 26, 26, 15, 15, 15, 10, 10, 10, 10, 3, 3, 3, 3, 9, 9, 9, 26, 26, 17, 26] 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]) total number of confs: 122 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001442465297 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297 Building ZINC001442465297 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442465297 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 698) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@H](C)c1cccc(C(F)(F)F)c1) `ZINC001442465297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442465297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001442465297 none COCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@H](C)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 6, 8, 10, 11, 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] 0 hydrogens 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, 7, 3, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 8, 8, 7, 7, 5, 5, 5, 5, 4, 4, 4, 12, 12, 12, 12] 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]) total number of confs: 61 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 699) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@H](C)c1cccc(C(F)(F)F)c1) `ZINC001442465297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442465297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001442465297 none COCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@H](C)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 6, 8, 10, 11, 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] 0 hydrogens 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, 10, 10, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 9, 9, 9, 26, 26, 17, 26, 26, 26, 26, 26, 26, 15, 15, 15, 10, 10, 10, 10, 3, 3, 3, 3, 9, 9, 9, 26, 26, 17, 26] 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]) total number of confs: 122 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001442465297 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465297 Building ZINC001442465301 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442465301 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/700 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@@H](C)c1cccc(C(F)(F)F)c1) `ZINC001442465301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442465301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001442465301 none COCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@@H](C)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 6, 8, 10, 11, 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] 0 hydrogens 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, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 25, 25, 18, 25, 25, 25, 25, 25, 25, 14, 14, 14, 10, 10, 10, 10, 4, 4, 4, 4, 9, 9, 9, 25, 25, 18, 25] 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]) total number of confs: 114 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/701 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/701' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@@H](C)c1cccc(C(F)(F)F)c1) `ZINC001442465301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442465301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001442465301 none COCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@@H](C)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 6, 8, 10, 11, 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] 0 hydrogens 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, 7, 3, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 4, 4, 4, 12, 12, 7, 12, 12, 12, 12, 12, 12, 11, 11, 11, 8, 8, 7, 7, 5, 5, 5, 5, 4, 4, 4, 12, 12, 7, 12] 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]) total number of confs: 72 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001442465301 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301 Building ZINC001442465301 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442465301 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 700) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@@H](C)c1cccc(C(F)(F)F)c1) `ZINC001442465301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442465301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001442465301 none COCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@@H](C)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 6, 8, 10, 11, 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] 0 hydrogens 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, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 25, 25, 18, 25, 25, 25, 25, 25, 25, 14, 14, 14, 10, 10, 10, 10, 4, 4, 4, 4, 9, 9, 9, 25, 25, 18, 25] 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]) total number of confs: 114 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 701) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@@H](C)c1cccc(C(F)(F)F)c1) `ZINC001442465301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442465301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001442465301 none COCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@@H](C)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 6, 8, 10, 11, 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] 0 hydrogens 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, 7, 3, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 4, 4, 4, 12, 12, 7, 12, 12, 12, 12, 12, 12, 11, 11, 11, 8, 8, 7, 7, 5, 5, 5, 5, 4, 4, 4, 12, 12, 7, 12] 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]) total number of confs: 72 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001442465301 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001442465301 Building ZINC001443058613 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443058613 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/702 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1c(Br)cc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001443058613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443058613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001443058613 none CCOc1c(Br)cc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 17, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 10, 10, 10, 10, 6, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 29, 29, 29, 29, 29, 10, 10, 3, 7, 7, 7, 7] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/703 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/703' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1c(Br)cc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001443058613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443058613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001443058613 none CCOc1c(Br)cc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 17, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 10, 10, 10, 10, 6, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 29, 29, 29, 29, 29, 10, 10, 3, 7, 7, 7, 7] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001443058613 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613 Building ZINC001443058613 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443058613 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 702) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCOc1c(Br)cc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001443058613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443058613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001443058613 none CCOc1c(Br)cc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 17, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 10, 10, 10, 10, 6, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 29, 29, 29, 29, 29, 10, 10, 3, 7, 7, 7, 7] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 703) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCOc1c(Br)cc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001443058613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443058613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001443058613 none CCOc1c(Br)cc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 17, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 10, 10, 10, 10, 6, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 29, 29, 29, 29, 29, 10, 10, 3, 7, 7, 7, 7] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001443058613 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443058613 Building ZINC001443303401 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443303401 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/704 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)Nc2cccc3c2CCN(C(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)C3)cc1) `ZINC001443303401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443303401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001443303401 none Cc1ccc(NC(=O)Nc2cccc3c2CCN(C(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)C3)cc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 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, 7, 4, 7, 6, 4, 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, 22, 28, 28, 22, 18, 18, 18, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 2, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 28, 28, 28, 28, 28, 28, 28, 22, 18, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 5, 5, 28, 28] 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, 52, 53, 54, 55, 56]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/705 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/705' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)Nc2cccc3c2CCN(C(=O)[C@]([O-])([SiH3])c2cccc(C)c2)C3)cc1) `ZINC001443303401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443303401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001443303401 none Cc1ccc(NC(=O)Nc2cccc3c2CCN(C(=O)[C@]([O-])([SiH3])c2cccc(C)c2)C3)cc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 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, 7, 4, 7, 6, 4, 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, 22, 28, 28, 22, 19, 19, 19, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 2, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 28, 28, 28, 28, 28, 28, 28, 22, 19, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 5, 5, 28, 28] 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, 52, 53, 54, 55, 56]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001443303401 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401 Building ZINC001443303401 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443303401 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 704) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(NC(=O)Nc2cccc3c2CCN(C(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)C3)cc1) `ZINC001443303401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443303401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001443303401 none Cc1ccc(NC(=O)Nc2cccc3c2CCN(C(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)C3)cc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 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, 7, 4, 7, 6, 4, 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, 22, 28, 28, 22, 18, 18, 18, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 2, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 28, 28, 28, 28, 28, 28, 28, 22, 18, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 5, 5, 28, 28] 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, 52, 53, 54, 55, 56]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 705) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(NC(=O)Nc2cccc3c2CCN(C(=O)[C@]([O-])([SiH3])c2cccc(C)c2)C3)cc1) `ZINC001443303401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443303401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001443303401 none Cc1ccc(NC(=O)Nc2cccc3c2CCN(C(=O)[C@]([O-])([SiH3])c2cccc(C)c2)C3)cc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 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, 7, 4, 7, 6, 4, 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, 22, 28, 28, 22, 19, 19, 19, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 2, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 28, 28, 28, 28, 28, 28, 28, 22, 19, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 5, 5, 28, 28] 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, 52, 53, 54, 55, 56]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001443303401 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443303401 Building ZINC001443311843 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443311843 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/706 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(OCCSc2ccc(Cl)cc2)cc1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001443311843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443311843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001443311843 none O=C(NCc1ccc(OCCSc2ccc(Cl)cc2)cc1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 14, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 10, 10, 5, 10, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 43, 43, 50, 50, 50, 50, 50, 50, 10, 10, 1, 1, 2, 1, 1] 100 rigid atoms, others: [0, 1, 2, 3, 45, 46, 48, 49, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/707 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/707' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(OCCSc2ccc(Cl)cc2)cc1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001443311843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443311843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001443311843 none O=C(NCc1ccc(OCCSc2ccc(Cl)cc2)cc1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 14, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 11, 11, 5, 11, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 11, 43, 43, 50, 50, 50, 50, 50, 50, 11, 11, 1, 1, 2, 1, 1] 100 rigid atoms, others: [0, 1, 2, 3, 45, 46, 48, 49, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001443311843 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843 Building ZINC001443311843 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443311843 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 706) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1ccc(OCCSc2ccc(Cl)cc2)cc1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001443311843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443311843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001443311843 none O=C(NCc1ccc(OCCSc2ccc(Cl)cc2)cc1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 14, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 10, 10, 5, 10, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 43, 43, 50, 50, 50, 50, 50, 50, 10, 10, 1, 1, 2, 1, 1] 100 rigid atoms, others: [0, 1, 2, 3, 45, 46, 48, 49, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 707) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1ccc(OCCSc2ccc(Cl)cc2)cc1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001443311843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443311843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001443311843 none O=C(NCc1ccc(OCCSc2ccc(Cl)cc2)cc1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 14, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 11, 11, 5, 11, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 11, 43, 43, 50, 50, 50, 50, 50, 50, 11, 11, 1, 1, 2, 1, 1] 100 rigid atoms, others: [0, 1, 2, 3, 45, 46, 48, 49, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001443311843 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443311843 Building ZINC001443479054 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443479054 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/708 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccn2)Cc2ccc(Br)cc2F)c1) `ZINC001443479054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443479054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001443479054 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccn2)Cc2ccc(Br)cc2F)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 15, 1, 7, 7, 7, 7, 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, 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: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 4, 10, 15, 15, 15, 15, 15, 4, 9, 16, 16, 12, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 10, 10, 15, 15, 15, 15, 9, 9, 16, 16, 16, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/709 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/709' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccn2)Cc2ccc(Br)cc2F)c1) `ZINC001443479054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443479054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001443479054 none Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccn2)Cc2ccc(Br)cc2F)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 15, 1, 7, 7, 7, 7, 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, 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: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 4, 10, 15, 15, 15, 15, 15, 4, 9, 16, 16, 12, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 10, 10, 15, 15, 15, 15, 9, 9, 16, 16, 16, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001443479054 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054 Building ZINC001443479054 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443479054 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 708) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccn2)Cc2ccc(Br)cc2F)c1) `ZINC001443479054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443479054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001443479054 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccn2)Cc2ccc(Br)cc2F)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 15, 1, 7, 7, 7, 7, 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, 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: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 4, 10, 15, 15, 15, 15, 15, 4, 9, 16, 16, 12, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 10, 10, 15, 15, 15, 15, 9, 9, 16, 16, 16, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 709) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccn2)Cc2ccc(Br)cc2F)c1) `ZINC001443479054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443479054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001443479054 none Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccn2)Cc2ccc(Br)cc2F)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 15, 1, 7, 7, 7, 7, 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, 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: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 4, 10, 15, 15, 15, 15, 15, 4, 9, 16, 16, 12, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 10, 10, 15, 15, 15, 15, 9, 9, 16, 16, 16, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001443479054 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443479054 Building ZINC001443503548 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443503548 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/710 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[nH]nc1c1ccc(Br)cc1) `ZINC001443503548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443503548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001443503548 none CCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[nH]nc1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.pl3', 'H', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 6, 8, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 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, 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: [23, 14, 14, 11, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 14, 14, 14, 14, 14, 29, 29, 23, 23, 29, 29, 23, 23, 23, 23, 23, 11, 10, 10, 29, 29, 29, 29] 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]) total number of confs: 143 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/711 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/711' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[nH]nc1c1ccc(Br)cc1) `ZINC001443503548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443503548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001443503548 none CCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[nH]nc1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.pl3', 'H', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 6, 8, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 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, 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: [22, 12, 12, 11, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 27, 27, 12, 12, 27, 27, 22, 22, 22, 22, 22, 11, 11, 11, 27, 27, 27, 27] 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]) total number of confs: 164 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001443503548 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548 Building ZINC001443503548 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443503548 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 710) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[nH]nc1c1ccc(Br)cc1) `ZINC001443503548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443503548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001443503548 none CCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)[nH]nc1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.pl3', 'H', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 6, 8, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 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, 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: [23, 14, 14, 11, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 14, 14, 14, 14, 14, 29, 29, 23, 23, 29, 29, 23, 23, 23, 23, 23, 11, 10, 10, 29, 29, 29, 29] 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]) total number of confs: 143 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 711) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[nH]nc1c1ccc(Br)cc1) `ZINC001443503548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443503548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001443503548 none CCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)[nH]nc1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.pl3', 'H', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 6, 8, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 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, 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: [22, 12, 12, 11, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 27, 27, 12, 12, 27, 27, 22, 22, 22, 22, 22, 11, 11, 11, 27, 27, 27, 27] 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]) total number of confs: 164 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001443503548 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443503548 Building ZINC001443603550 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443603550 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/712 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(F)cc2)sc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001443603550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443603550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001443603550 none Cc1nc(c2ccc(F)cc2)sc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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.pl3', 'H', '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'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 26, 26, 26, 26, 20, 9, 5, 9, 9, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 20, 26, 26, 26, 26, 9, 9, 9, 5, 8, 8, 8, 8] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/713 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/713' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(F)cc2)sc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001443603550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443603550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001443603550 none Cc1nc(c2ccc(F)cc2)sc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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.pl3', 'H', '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'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 24, 24, 23, 24, 24, 24, 16, 8, 5, 8, 8, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 24, 24, 24, 24, 8, 8, 8, 5, 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, 45, 46]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001443603550 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550 Building ZINC001443603550 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443603550 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 712) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nc(c2ccc(F)cc2)sc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001443603550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443603550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001443603550 none Cc1nc(c2ccc(F)cc2)sc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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.pl3', 'H', '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'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 26, 26, 26, 26, 20, 9, 5, 9, 9, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 20, 26, 26, 26, 26, 9, 9, 9, 5, 8, 8, 8, 8] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 713) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nc(c2ccc(F)cc2)sc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001443603550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443603550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001443603550 none Cc1nc(c2ccc(F)cc2)sc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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.pl3', 'H', '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'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 24, 24, 23, 24, 24, 24, 16, 8, 5, 8, 8, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 24, 24, 24, 24, 8, 8, 8, 5, 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, 45, 46]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001443603550 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603550 Building ZINC001443603555 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443603555 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/714 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(F)cc2)sc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001443603555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443603555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001443603555 none Cc1nc(c2ccc(F)cc2)sc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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.pl3', 'H', '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'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 17, 17, 17, 25, 25, 25, 25, 25, 25, 17, 9, 5, 9, 9, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 25, 25, 25, 25, 9, 9, 9, 5, 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, 45, 46]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/715 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/715' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(F)cc2)sc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001443603555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443603555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001443603555 none Cc1nc(c2ccc(F)cc2)sc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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.pl3', 'H', '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'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 28, 28, 28, 28, 28, 28, 19, 9, 5, 9, 9, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 19, 19, 19, 28, 28, 28, 28, 9, 9, 9, 5, 8, 8, 8, 8] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001443603555 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555 Building ZINC001443603555 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443603555 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 714) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nc(c2ccc(F)cc2)sc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001443603555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443603555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001443603555 none Cc1nc(c2ccc(F)cc2)sc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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.pl3', 'H', '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'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 17, 17, 17, 25, 25, 25, 25, 25, 25, 17, 9, 5, 9, 9, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 25, 25, 25, 25, 9, 9, 9, 5, 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, 45, 46]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 715) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nc(c2ccc(F)cc2)sc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001443603555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443603555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001443603555 none Cc1nc(c2ccc(F)cc2)sc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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.pl3', 'H', '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'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 28, 28, 28, 28, 28, 28, 19, 9, 5, 9, 9, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 19, 19, 19, 28, 28, 28, 28, 9, 9, 9, 5, 8, 8, 8, 8] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001443603555 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443603555 Building ZINC001443608729 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443608729 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/716 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@@H](c1cccnc1)c1ccc(F)c(F)c1) `ZINC001443608729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443608729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001443608729 none CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@@H](c1cccnc1)c1ccc(F)c(F)c1 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 15, 1, 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, 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, 7, 7, 7] 0 hydrogens 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, 5, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 15, 15, 15, 15, 15, 7, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15] 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, 49]) total number of confs: 62 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/717 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/717' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@@H](c1cccnc1)c1ccc(F)c(F)c1) `ZINC001443608729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443608729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001443608729 none CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@@H](c1cccnc1)c1ccc(F)c(F)c1 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 15, 1, 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, 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, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 6, 6, 10, 10, 10, 10, 10, 6, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 14, 14, 14] 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, 49]) total number of confs: 57 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001443608729 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729 Building ZINC001443608729 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443608729 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 716) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@@H](c1cccnc1)c1ccc(F)c(F)c1) `ZINC001443608729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443608729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001443608729 none CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@@H](c1cccnc1)c1ccc(F)c(F)c1 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 15, 1, 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, 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, 7, 7, 7] 0 hydrogens 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, 5, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 15, 15, 15, 15, 15, 7, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15] 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, 49]) total number of confs: 62 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 717) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@@H](c1cccnc1)c1ccc(F)c(F)c1) `ZINC001443608729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443608729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001443608729 none CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@@H](c1cccnc1)c1ccc(F)c(F)c1 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 15, 1, 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, 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, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 6, 6, 10, 10, 10, 10, 10, 6, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 14, 14, 14] 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, 49]) total number of confs: 57 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001443608729 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608729 Building ZINC001443608733 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443608733 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/718 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@H](c1cccnc1)c1ccc(F)c(F)c1) `ZINC001443608733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443608733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001443608733 none CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@H](c1cccnc1)c1ccc(F)c(F)c1 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 15, 1, 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, 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, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 6, 6, 10, 10, 10, 10, 10, 6, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 14, 14, 14] 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, 49]) total number of confs: 57 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/719 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/719' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@H](c1cccnc1)c1ccc(F)c(F)c1) `ZINC001443608733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443608733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001443608733 none CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@H](c1cccnc1)c1ccc(F)c(F)c1 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 15, 1, 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, 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, 7, 7, 7] 0 hydrogens 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, 5, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 15, 15, 15, 15, 15, 7, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 5, 5, 5, 5, 15, 15, 15, 15, 16, 16, 16] 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, 49]) total number of confs: 63 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001443608733 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733 Building ZINC001443608733 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443608733 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 718) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@H](c1cccnc1)c1ccc(F)c(F)c1) `ZINC001443608733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443608733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001443608733 none CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@H](c1cccnc1)c1ccc(F)c(F)c1 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 15, 1, 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, 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, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 6, 6, 10, 10, 10, 10, 10, 6, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 14, 14, 14] 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, 49]) total number of confs: 57 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 719) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@H](c1cccnc1)c1ccc(F)c(F)c1) `ZINC001443608733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443608733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001443608733 none CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@H](c1cccnc1)c1ccc(F)c(F)c1 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 15, 1, 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, 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, 7, 7, 7] 0 hydrogens 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, 5, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 15, 15, 15, 15, 15, 7, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 5, 5, 5, 5, 15, 15, 15, 15, 16, 16, 16] 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, 49]) total number of confs: 63 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001443608733 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001443608733 Building ZINC001444135033 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001444135033 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/720 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C2(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CCCCC2)cc1OC) `ZINC001444135033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001444135033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001444135033 none COc1ccc(C2(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CCCCC2)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.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 5, 5, 1, 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, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 22, 22, 22, 22, 16, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 22, 22, 22, 33, 34, 34, 34, 22, 22, 9, 9, 3, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 22, 33, 33, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/721 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/721' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C2(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CCCCC2)cc1OC) `ZINC001444135033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001444135033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001444135033 none COc1ccc(C2(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CCCCC2)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.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 5, 5, 1, 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, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 20, 20, 20, 20, 14, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 20, 20, 20, 33, 34, 34, 34, 20, 20, 8, 8, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 20, 33, 33, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001444135033 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033 Building ZINC001444135033 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001444135033 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 720) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc(C2(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CCCCC2)cc1OC) `ZINC001444135033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001444135033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001444135033 none COc1ccc(C2(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CCCCC2)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.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 5, 5, 1, 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, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 22, 22, 22, 22, 16, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 22, 22, 22, 33, 34, 34, 34, 22, 22, 9, 9, 3, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 22, 33, 33, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 721) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc(C2(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CCCCC2)cc1OC) `ZINC001444135033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001444135033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001444135033 none COc1ccc(C2(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CCCCC2)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.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 5, 5, 1, 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, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 20, 20, 20, 20, 14, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 20, 20, 20, 33, 34, 34, 34, 20, 20, 8, 8, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 20, 33, 33, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001444135033 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444135033 Building ZINC001444355030 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001444355030 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/722 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1) `ZINC001444355030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001444355030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001444355030 none CN(C)C[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 5, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 3, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 8, 8, 2, 2, 1, 2, 8, 8, 31, 31, 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, 53]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/723 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/723' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1) `ZINC001444355030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001444355030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001444355030 none CN(C)C[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 5, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 12, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 8, 8, 2, 2, 2, 2, 8, 8, 31, 31, 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, 53]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/724 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/724' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1) `ZINC001444355030.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001444355030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/2/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'} 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 57 natoms 56 natoms 55 natoms 54 names: ZINC001444355030 none CN(C)C[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 5, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 12, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 8, 8, 2, 2, 1, 2, 8, 8, 32, 32, 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, 53]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/725 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/725' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1) `ZINC001444355030.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001444355030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/3/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'} 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 57 natoms 56 natoms 55 natoms 54 names: ZINC001444355030 none CN(C)C[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 5, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 12, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 8, 8, 2, 2, 1, 2, 8, 8, 32, 32, 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, 53]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001444355030 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 Building ZINC001444355030 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001444355030 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 722) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(C)C[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1) `ZINC001444355030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001444355030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001444355030 none CN(C)C[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 5, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 3, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 8, 8, 2, 2, 1, 2, 8, 8, 31, 31, 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, 53]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 723) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(C)C[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1) `ZINC001444355030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001444355030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001444355030 none CN(C)C[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 5, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 12, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 8, 8, 2, 2, 2, 2, 8, 8, 31, 31, 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, 53]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 724) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/724: 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(C)C[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1) `ZINC001444355030.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001444355030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/2/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'} 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 57 natoms 56 natoms 55 natoms 54 names: ZINC001444355030 none CN(C)C[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 5, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 12, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 8, 8, 2, 2, 1, 2, 8, 8, 32, 32, 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, 53]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 725) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/725: 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(C)C[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1) `ZINC001444355030.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001444355030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/3/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'} 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 57 natoms 56 natoms 55 natoms 54 names: ZINC001444355030 none CN(C)C[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 5, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 12, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 8, 8, 2, 2, 1, 2, 8, 8, 32, 32, 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, 53]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001444355030 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 Building ZINC001444355030 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001444355030 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 722) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(C)C[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1) `ZINC001444355030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001444355030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001444355030 none CN(C)C[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 5, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 3, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 8, 8, 2, 2, 1, 2, 8, 8, 31, 31, 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, 53]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 723) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(C)C[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1) `ZINC001444355030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001444355030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001444355030 none CN(C)C[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 5, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 12, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 8, 8, 2, 2, 2, 2, 8, 8, 31, 31, 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, 53]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 724) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/724: 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(C)C[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1) `ZINC001444355030.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001444355030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/2/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'} 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 57 natoms 56 natoms 55 natoms 54 names: ZINC001444355030 none CN(C)C[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 5, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 12, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 8, 8, 2, 2, 1, 2, 8, 8, 32, 32, 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, 53]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 725) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/725: 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(C)C[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1) `ZINC001444355030.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001444355030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/3/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'} 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 57 natoms 56 natoms 55 natoms 54 names: ZINC001444355030 none CN(C)C[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 5, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 12, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 8, 8, 2, 2, 1, 2, 8, 8, 32, 32, 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, 53]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001444355030 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 Building ZINC001444355030 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001444355030 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 722) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(C)C[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1) `ZINC001444355030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001444355030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001444355030 none CN(C)C[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 5, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 3, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 8, 8, 2, 2, 1, 2, 8, 8, 31, 31, 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, 53]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 723) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(C)C[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1) `ZINC001444355030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001444355030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001444355030 none CN(C)C[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 5, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 12, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 8, 8, 2, 2, 2, 2, 8, 8, 31, 31, 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, 53]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 724) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/724: 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(C)C[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1) `ZINC001444355030.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001444355030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/2/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'} 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 57 natoms 56 natoms 55 natoms 54 names: ZINC001444355030 none CN(C)C[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 5, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 12, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 8, 8, 2, 2, 1, 2, 8, 8, 32, 32, 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, 53]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 725) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/725: 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(C)C[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1) `ZINC001444355030.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001444355030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/3/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'} 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 57 natoms 56 natoms 55 natoms 54 names: ZINC001444355030 none CN(C)C[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 5, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 12, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 8, 8, 2, 2, 1, 2, 8, 8, 32, 32, 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, 53]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001444355030 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444355030 Building ZINC001444897604 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001444897604 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/726 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1csc(c2ccc(C(F)(F)F)cc2)n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001444897604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001444897604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001444897604 none O=C(NCc1csc(c2ccc(C(F)(F)F)cc2)n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 14, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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] 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] 0 hydrogens need 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, 30, 30, 30, 30, 32, 32, 31, 32, 32, 32, 32, 32, 32, 30, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 30, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/727 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/727' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1csc(c2ccc(C(F)(F)F)cc2)n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001444897604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001444897604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001444897604 none O=C(NCc1csc(c2ccc(C(F)(F)F)cc2)n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 14, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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] 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] 0 hydrogens need 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, 30, 30, 30, 30, 31, 31, 30, 31, 31, 31, 31, 31, 31, 30, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 30, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001444897604 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604 Building ZINC001444897604 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001444897604 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 726) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1csc(c2ccc(C(F)(F)F)cc2)n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001444897604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001444897604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001444897604 none O=C(NCc1csc(c2ccc(C(F)(F)F)cc2)n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 14, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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] 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] 0 hydrogens need 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, 30, 30, 30, 30, 32, 32, 31, 32, 32, 32, 32, 32, 32, 30, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 30, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 727) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1csc(c2ccc(C(F)(F)F)cc2)n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001444897604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001444897604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001444897604 none O=C(NCc1csc(c2ccc(C(F)(F)F)cc2)n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 14, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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] 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] 0 hydrogens need 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, 30, 30, 30, 30, 31, 31, 30, 31, 31, 31, 31, 31, 31, 30, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 30, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001444897604 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001444897604 Building ZINC001445218257 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001445218257 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/728 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CNC(=O)Nc2ccccc2Cl)c1) `ZINC001445218257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445218257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001445218257 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CNC(=O)Nc2ccccc2Cl)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.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', 'H', '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, 1, 1, 1, 1, 1, 5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 10, 10, 10, 21, 31, 31, 31, 35, 50, 50, 47, 50, 50, 50, 10, 2, 2, 2, 2, 2, 2, 3, 10, 10, 10, 21, 21, 31, 35, 50, 50, 50, 50, 10] 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: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/729 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/729' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc(CNC(=O)Nc2ccccc2Cl)c1) `ZINC001445218257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445218257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001445218257 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc(CNC(=O)Nc2ccccc2Cl)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.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', 'H', '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, 1, 1, 1, 1, 1, 5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 10, 10, 10, 22, 34, 34, 34, 38, 50, 50, 39, 50, 50, 50, 10, 2, 2, 2, 2, 2, 2, 3, 10, 10, 10, 22, 22, 34, 38, 50, 50, 50, 50, 10] 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: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001445218257 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257 Building ZINC001445218257 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001445218257 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 728) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CNC(=O)Nc2ccccc2Cl)c1) `ZINC001445218257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445218257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001445218257 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CNC(=O)Nc2ccccc2Cl)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.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', 'H', '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, 1, 1, 1, 1, 1, 5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 10, 10, 10, 21, 31, 31, 31, 35, 50, 50, 47, 50, 50, 50, 10, 2, 2, 2, 2, 2, 2, 3, 10, 10, 10, 21, 21, 31, 35, 50, 50, 50, 50, 10] 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: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 729) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc(CNC(=O)Nc2ccccc2Cl)c1) `ZINC001445218257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445218257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001445218257 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc(CNC(=O)Nc2ccccc2Cl)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.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', 'H', '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, 1, 1, 1, 1, 1, 5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 10, 10, 10, 22, 34, 34, 34, 38, 50, 50, 39, 50, 50, 50, 10, 2, 2, 2, 2, 2, 2, 3, 10, 10, 10, 22, 22, 34, 38, 50, 50, 50, 50, 10] 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: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001445218257 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445218257 Building ZINC001445222925 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001445222925 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/730 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2NC(C)C)cc1Cl) `ZINC001445222925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445222925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001445222925 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2NC(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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 1, 8, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 17, 23, 23, 6, 6, 6, 12, 12, 12, 6, 6, 2, 6, 6, 6, 17, 23, 23, 23, 23, 23, 23, 23, 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, 40, 41, 42]) total number of confs: 123 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/731 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/731' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2NC(C)C)cc1Cl) `ZINC001445222925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445222925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001445222925 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2NC(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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 1, 8, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 17, 23, 23, 6, 6, 6, 12, 12, 12, 6, 6, 2, 6, 6, 6, 17, 23, 23, 23, 23, 23, 23, 23, 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, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001445222925 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925 Building ZINC001445222925 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001445222925 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 730) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2NC(C)C)cc1Cl) `ZINC001445222925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445222925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001445222925 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2NC(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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 1, 8, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 17, 23, 23, 6, 6, 6, 12, 12, 12, 6, 6, 2, 6, 6, 6, 17, 23, 23, 23, 23, 23, 23, 23, 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, 40, 41, 42]) total number of confs: 123 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 731) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2NC(C)C)cc1Cl) `ZINC001445222925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445222925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001445222925 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2NC(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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 1, 8, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 17, 23, 23, 6, 6, 6, 12, 12, 12, 6, 6, 2, 6, 6, 6, 17, 23, 23, 23, 23, 23, 23, 23, 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, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001445222925 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445222925 Building ZINC001445636479 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001445636479 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/732 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1CCN(C(=O)OC(C)(C)C)CC1) `ZINC001445636479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445636479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001445636479 none CCCN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 8, 1, 11, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 0 hydrogens 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, 12, 7, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 11, 11, 11, 11, 20, 20, 33, 33, 33, 33, 11, 11, 14, 14, 14, 14, 14, 12, 12, 3, 1, 3, 11, 11, 11, 11, 11, 33, 33, 33, 33, 33, 33, 33, 33, 33, 11, 11, 11, 11] 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 126 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/733 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/733' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1CCN(C(=O)OC(C)(C)C)CC1) `ZINC001445636479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445636479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001445636479 none CCCN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 8, 1, 11, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 0 hydrogens 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, 11, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 10, 10, 10, 10, 22, 22, 35, 35, 35, 35, 10, 10, 13, 13, 13, 13, 13, 11, 11, 3, 1, 3, 10, 10, 10, 10, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 10, 10, 10, 10] 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 135 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001445636479 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479 Building ZINC001445636479 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001445636479 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 732) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1CCN(C(=O)OC(C)(C)C)CC1) `ZINC001445636479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445636479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001445636479 none CCCN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 8, 1, 11, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 0 hydrogens 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, 12, 7, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 11, 11, 11, 11, 20, 20, 33, 33, 33, 33, 11, 11, 14, 14, 14, 14, 14, 12, 12, 3, 1, 3, 11, 11, 11, 11, 11, 33, 33, 33, 33, 33, 33, 33, 33, 33, 11, 11, 11, 11] 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 126 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 733) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1CCN(C(=O)OC(C)(C)C)CC1) `ZINC001445636479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445636479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001445636479 none CCCN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 8, 1, 11, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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] 0 hydrogens 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, 11, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 10, 10, 10, 10, 22, 22, 35, 35, 35, 35, 10, 10, 13, 13, 13, 13, 13, 11, 11, 3, 1, 3, 10, 10, 10, 10, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 10, 10, 10, 10] 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 135 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001445636479 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001445636479 Building ZINC001446436612 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446436612 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/734 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc2cccnc2cc1Br)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001446436612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446436612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001446436612 none O=C(NCc1cc2cccnc2cc1Br)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 18, 18, 43, 43, 43, 43, 43, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/735 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/735' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc2cccnc2cc1Br)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001446436612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446436612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001446436612 none O=C(NCc1cc2cccnc2cc1Br)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 19, 19, 43, 43, 43, 43, 43, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001446436612 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612 Building ZINC001446436612 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446436612 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 734) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1cc2cccnc2cc1Br)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001446436612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446436612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001446436612 none O=C(NCc1cc2cccnc2cc1Br)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 18, 18, 43, 43, 43, 43, 43, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 735) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1cc2cccnc2cc1Br)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001446436612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446436612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001446436612 none O=C(NCc1cc2cccnc2cc1Br)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 19, 19, 43, 43, 43, 43, 43, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001446436612 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446436612 Building ZINC001446754562 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446754562 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/736 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(F)c1) `ZINC001446754562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446754562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001446754562 none CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', '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', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 4, 4, 4, 4, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 4, 21, 21, 21, 21] 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, 54, 55, 56]) total number of confs: 81 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/737 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/737' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(F)c1) `ZINC001446754562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446754562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001446754562 none CCCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', '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', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 4, 4, 4, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 8, 8, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 4, 21, 21, 21, 21] 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, 54, 55, 56]) total number of confs: 79 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001446754562 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562 Building ZINC001446754562 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446754562 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 736) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(F)c1) `ZINC001446754562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446754562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001446754562 none CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', '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', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 4, 4, 4, 4, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 4, 21, 21, 21, 21] 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, 54, 55, 56]) total number of confs: 81 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 737) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(F)c1) `ZINC001446754562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446754562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001446754562 none CCCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', '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', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 4, 4, 4, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 8, 8, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 4, 21, 21, 21, 21] 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, 54, 55, 56]) total number of confs: 79 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001446754562 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446754562 Building ZINC001446883125 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446883125 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/738 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nn1c1ccc(Cl)cc1Cl) `ZINC001446883125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446883125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001446883125 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nn1c1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 6, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 9, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 22, 22, 19, 22, 22, 22, 22, 9, 9, 9, 9, 4, 7, 7, 7, 7, 22, 22, 22] 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/739 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/739' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nn1c1ccc(Cl)cc1Cl) `ZINC001446883125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446883125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001446883125 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nn1c1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 6, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 9, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 22, 22, 18, 21, 22, 22, 22, 9, 9, 9, 9, 4, 7, 7, 7, 7, 22, 22, 22] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001446883125 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125 Building ZINC001446883125 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446883125 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 738) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nn1c1ccc(Cl)cc1Cl) `ZINC001446883125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446883125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001446883125 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nn1c1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 6, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 9, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 22, 22, 19, 22, 22, 22, 22, 9, 9, 9, 9, 4, 7, 7, 7, 7, 22, 22, 22] 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 739) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nn1c1ccc(Cl)cc1Cl) `ZINC001446883125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446883125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001446883125 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nn1c1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 6, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 9, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 22, 22, 18, 21, 22, 22, 22, 9, 9, 9, 9, 4, 7, 7, 7, 7, 22, 22, 22] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001446883125 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446883125 Building ZINC001446993036 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446993036 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/740 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/740' -> `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])c1cc(Cl)cc(Cl)c1) `ZINC001446993036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446993036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001446993036 none O=C(N1CCC[C@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.ar', 'C.ar', 'C.ar', 'Cl', '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'] 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, 1, 16, 1, 1, 16, 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: [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] 0 hydrogens need 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, 23, 23, 23, 23, 25, 49, 49, 49, 49, 49, 23, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 2, 2, 2, 2, 2, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 3, 1, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/741 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/741' -> `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])c1cc(Cl)cc(Cl)c1) `ZINC001446993036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446993036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001446993036 none O=C(N1CCC[C@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.ar', 'C.ar', 'C.ar', 'Cl', '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'] 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, 1, 16, 1, 1, 16, 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: [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] 0 hydrogens need 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, 21, 21, 21, 21, 27, 50, 50, 50, 50, 50, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1] 50 rigid atoms, others: [1, 50, 51, 52, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001446993036 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036 Building ZINC001446993036 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446993036 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 740) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCC[C@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001446993036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446993036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001446993036 none O=C(N1CCC[C@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.ar', 'C.ar', 'C.ar', 'Cl', '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'] 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, 1, 16, 1, 1, 16, 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: [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] 0 hydrogens need 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, 23, 23, 23, 23, 25, 49, 49, 49, 49, 49, 23, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 2, 2, 2, 2, 2, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 3, 1, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 741) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCC[C@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001446993036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446993036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001446993036 none O=C(N1CCC[C@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.ar', 'C.ar', 'C.ar', 'Cl', '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'] 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, 1, 16, 1, 1, 16, 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: [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] 0 hydrogens need 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, 21, 21, 21, 21, 27, 50, 50, 50, 50, 50, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1] 50 rigid atoms, others: [1, 50, 51, 52, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001446993036 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993036 Building ZINC001446993039 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446993039 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/742 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/742' -> `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])c1cc(Cl)cc(Cl)c1) `ZINC001446993039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446993039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001446993039 none O=C(N1CCC[C@@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.ar', 'C.ar', 'C.ar', 'Cl', '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'] 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, 1, 16, 1, 1, 16, 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: [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] 0 hydrogens need 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, 23, 23, 23, 23, 27, 50, 50, 50, 50, 50, 23, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1] 50 rigid atoms, others: [1, 50, 51, 52, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/743 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/743' -> `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])c1cc(Cl)cc(Cl)c1) `ZINC001446993039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446993039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001446993039 none O=C(N1CCC[C@@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.ar', 'C.ar', 'C.ar', 'Cl', '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'] 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, 1, 16, 1, 1, 16, 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: [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] 0 hydrogens need 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, 23, 23, 23, 23, 25, 49, 49, 49, 49, 49, 23, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 2, 2, 2, 2, 2, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 3, 1, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001446993039 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039 Building ZINC001446993039 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446993039 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 742) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCC[C@@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001446993039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446993039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001446993039 none O=C(N1CCC[C@@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.ar', 'C.ar', 'C.ar', 'Cl', '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'] 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, 1, 16, 1, 1, 16, 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: [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] 0 hydrogens need 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, 23, 23, 23, 23, 27, 50, 50, 50, 50, 50, 23, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1] 50 rigid atoms, others: [1, 50, 51, 52, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 743) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCC[C@@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001446993039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446993039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001446993039 none O=C(N1CCC[C@@H](c2n[nH]c(C3CCCCC3)n2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.ar', 'C.ar', 'C.ar', 'Cl', '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'] 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, 1, 16, 1, 1, 16, 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: [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] 0 hydrogens need 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, 23, 23, 23, 23, 25, 49, 49, 49, 49, 49, 23, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 2, 2, 2, 2, 2, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 3, 1, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001446993039 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001446993039 Building ZINC001447396156 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001447396156 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/744 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)cc1Cl) `ZINC001447396156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001447396156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396156 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 10, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 5, 5, 5, 7, 7, 7, 5, 5, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 5] 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, 53, 54, 55, 56]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/745 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/745' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)cc1Cl) `ZINC001447396156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001447396156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396156 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 10, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 5, 5, 5, 7, 7, 7, 5, 5, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 5] 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, 53, 54, 55, 56]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/746 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/746' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)cc1Cl) `ZINC001447396156.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001447396156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/2/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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396156 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 4, 4, 4, 4, 4, 4, 4, 10, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4] 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, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/747 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/747' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)cc1Cl) `ZINC001447396156.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001447396156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/3/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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396156 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 4, 4, 4, 4, 4, 4, 4, 10, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4] 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, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001447396156 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 Building ZINC001447396156 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001447396156 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 744) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)cc1Cl) `ZINC001447396156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001447396156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396156 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 10, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 5, 5, 5, 7, 7, 7, 5, 5, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 5] 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, 53, 54, 55, 56]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 745) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)cc1Cl) `ZINC001447396156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001447396156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396156 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 10, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 5, 5, 5, 7, 7, 7, 5, 5, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 5] 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, 53, 54, 55, 56]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 746) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/746: 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)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)cc1Cl) `ZINC001447396156.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001447396156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/2/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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396156 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 4, 4, 4, 4, 4, 4, 4, 10, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4] 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, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 747) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/747: 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)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)cc1Cl) `ZINC001447396156.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001447396156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/3/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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396156 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 4, 4, 4, 4, 4, 4, 4, 10, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4] 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, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001447396156 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 Building ZINC001447396156 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001447396156 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 744) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)cc1Cl) `ZINC001447396156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001447396156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396156 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 10, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 5, 5, 5, 7, 7, 7, 5, 5, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 5] 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, 53, 54, 55, 56]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 745) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)cc1Cl) `ZINC001447396156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001447396156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396156 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 10, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 5, 5, 5, 7, 7, 7, 5, 5, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 5] 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, 53, 54, 55, 56]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 746) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/746: 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)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)cc1Cl) `ZINC001447396156.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001447396156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/2/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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396156 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 4, 4, 4, 4, 4, 4, 4, 10, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4] 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, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 747) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/747: 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)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)cc1Cl) `ZINC001447396156.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001447396156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/3/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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396156 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 4, 4, 4, 4, 4, 4, 4, 10, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4] 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, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001447396156 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 Building ZINC001447396156 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001447396156 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 744) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)cc1Cl) `ZINC001447396156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001447396156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396156 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 10, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 5, 5, 5, 7, 7, 7, 5, 5, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 5] 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, 53, 54, 55, 56]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 745) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)cc1Cl) `ZINC001447396156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001447396156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396156 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 10, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 5, 5, 5, 7, 7, 7, 5, 5, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 5] 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, 53, 54, 55, 56]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 746) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/746: 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)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)cc1Cl) `ZINC001447396156.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001447396156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/2/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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396156 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 4, 4, 4, 4, 4, 4, 4, 10, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4] 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, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 747) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/747: 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)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)cc1Cl) `ZINC001447396156.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001447396156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/3/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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396156 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 4, 4, 4, 4, 4, 4, 4, 10, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4] 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, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001447396156 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396156 Building ZINC001447396159 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001447396159 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/748 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)cc1Cl) `ZINC001447396159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001447396159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396159 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 4, 4, 4, 4, 4, 4, 4, 9, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4] 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, 53, 54, 55, 56]) total number of confs: 63 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/749 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/749' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)cc1Cl) `ZINC001447396159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001447396159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396159 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 4, 4, 4, 4, 4, 4, 4, 9, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4] 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, 53, 54, 55, 56]) total number of confs: 63 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/750 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/750' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)cc1Cl) `ZINC001447396159.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001447396159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/2/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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396159 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 9, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 5, 5, 5, 8, 8, 8, 5, 5, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 5] 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, 53, 54, 55, 56]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/751 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/751' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)cc1Cl) `ZINC001447396159.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001447396159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/3/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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396159 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 9, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 5, 5, 5, 8, 8, 8, 5, 5, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 5] 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, 53, 54, 55, 56]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001447396159 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 Building ZINC001447396159 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001447396159 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 748) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)cc1Cl) `ZINC001447396159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001447396159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396159 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 4, 4, 4, 4, 4, 4, 4, 9, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4] 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, 53, 54, 55, 56]) total number of confs: 63 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 749) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)cc1Cl) `ZINC001447396159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001447396159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396159 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 4, 4, 4, 4, 4, 4, 4, 9, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4] 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, 53, 54, 55, 56]) total number of confs: 63 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 750) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/750: 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)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)cc1Cl) `ZINC001447396159.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001447396159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/2/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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396159 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 9, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 5, 5, 5, 8, 8, 8, 5, 5, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 5] 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, 53, 54, 55, 56]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 751) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/751: 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)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)cc1Cl) `ZINC001447396159.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001447396159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/3/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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396159 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 9, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 5, 5, 5, 8, 8, 8, 5, 5, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 5] 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, 53, 54, 55, 56]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001447396159 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 Building ZINC001447396159 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001447396159 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 748) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)cc1Cl) `ZINC001447396159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001447396159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396159 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 4, 4, 4, 4, 4, 4, 4, 9, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4] 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, 53, 54, 55, 56]) total number of confs: 63 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 749) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)cc1Cl) `ZINC001447396159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001447396159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396159 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 4, 4, 4, 4, 4, 4, 4, 9, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4] 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, 53, 54, 55, 56]) total number of confs: 63 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 750) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/750: 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)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)cc1Cl) `ZINC001447396159.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001447396159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/2/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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396159 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 9, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 5, 5, 5, 8, 8, 8, 5, 5, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 5] 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, 53, 54, 55, 56]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 751) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/751: 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)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)cc1Cl) `ZINC001447396159.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001447396159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/3/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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396159 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 9, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 5, 5, 5, 8, 8, 8, 5, 5, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 5] 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, 53, 54, 55, 56]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001447396159 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 Building ZINC001447396159 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001447396159 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 748) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)cc1Cl) `ZINC001447396159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001447396159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396159 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 4, 4, 4, 4, 4, 4, 4, 9, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4] 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, 53, 54, 55, 56]) total number of confs: 63 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 749) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)cc1Cl) `ZINC001447396159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001447396159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396159 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 4, 4, 4, 4, 4, 4, 4, 9, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4] 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, 53, 54, 55, 56]) total number of confs: 63 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 750) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/750: 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)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)cc1Cl) `ZINC001447396159.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001447396159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/2/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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396159 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 9, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 5, 5, 5, 8, 8, 8, 5, 5, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 5] 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, 53, 54, 55, 56]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 751) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/751: 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)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)cc1Cl) `ZINC001447396159.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001447396159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/3/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 60 natoms 59 natoms 58 natoms 57 names: ZINC001447396159 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(N4CCCC[C@H]4C)ccc32)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 9, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 5, 5, 5, 8, 8, 8, 5, 5, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 5] 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, 53, 54, 55, 56]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001447396159 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447396159 Building ZINC001447988786 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001447988786 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/752 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2cccc(OC(F)F)c2)c1) `ZINC001447988786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001447988786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001447988786 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2cccc(OC(F)F)c2)c1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 3, 4, 5, 5, 5, 10, 10, 10, 10, 10, 31, 31, 31, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 10, 10, 10, 31, 10, 4] 150 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]) total number of confs: 82 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/753 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/753' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2cccc(OC(F)F)c2)c1) `ZINC001447988786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001447988786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001447988786 none Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2cccc(OC(F)F)c2)c1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 11, 11, 11, 11, 11, 28, 28, 28, 11, 4, 4, 4, 4, 2, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 11, 11, 11, 28, 11, 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, 53, 54]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001447988786 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786 Building ZINC001447988786 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001447988786 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 752) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2cccc(OC(F)F)c2)c1) `ZINC001447988786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001447988786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001447988786 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2cccc(OC(F)F)c2)c1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 3, 4, 5, 5, 5, 10, 10, 10, 10, 10, 31, 31, 31, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 10, 10, 10, 31, 10, 4] 150 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]) total number of confs: 82 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 753) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2cccc(OC(F)F)c2)c1) `ZINC001447988786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001447988786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001447988786 none Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2cccc(OC(F)F)c2)c1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 11, 11, 11, 11, 11, 28, 28, 28, 11, 4, 4, 4, 4, 2, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 11, 11, 11, 28, 11, 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, 53, 54]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001447988786 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988786 Building ZINC001447988791 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001447988791 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/754 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2cccc(OC(F)F)c2)c1) `ZINC001447988791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001447988791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001447988791 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2cccc(OC(F)F)c2)c1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 3, 3, 5, 5, 5, 12, 12, 12, 12, 12, 27, 27, 27, 12, 4, 4, 4, 4, 2, 4, 4, 5, 5, 5, 5, 5, 5, 5, 3, 3, 15, 12, 12, 12, 27, 12, 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, 53, 54]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/755 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/755' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2cccc(OC(F)F)c2)c1) `ZINC001447988791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001447988791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001447988791 none Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2cccc(OC(F)F)c2)c1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 2, 4, 4, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 2, 3, 4, 4, 4, 9, 9, 9, 9, 9, 27, 27, 27, 9, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 12, 9, 9, 9, 27, 9, 4] 150 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]) total number of confs: 85 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001447988791 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791 Building ZINC001447988791 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001447988791 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 754) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2cccc(OC(F)F)c2)c1) `ZINC001447988791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001447988791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001447988791 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2cccc(OC(F)F)c2)c1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 3, 3, 5, 5, 5, 12, 12, 12, 12, 12, 27, 27, 27, 12, 4, 4, 4, 4, 2, 4, 4, 5, 5, 5, 5, 5, 5, 5, 3, 3, 15, 12, 12, 12, 27, 12, 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, 53, 54]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 755) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2cccc(OC(F)F)c2)c1) `ZINC001447988791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001447988791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001447988791 none Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2cccc(OC(F)F)c2)c1 NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 2, 4, 4, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 2, 3, 4, 4, 4, 9, 9, 9, 9, 9, 27, 27, 27, 9, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 12, 9, 9, 9, 27, 9, 4] 150 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]) total number of confs: 85 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001447988791 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001447988791 Building ZINC001448072498 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448072498 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/756 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(C(F)(F)F)c1) `ZINC001448072498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448072498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001448072498 none CN(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 30, 13, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 46, 46, 37, 46, 46, 46, 46, 46, 46, 30, 30, 30, 30, 30, 30, 13, 13, 4, 3, 1, 3, 46, 46, 37, 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]) total number of confs: 186 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/757 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/757' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(C(F)(F)F)c1) `ZINC001448072498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448072498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001448072498 none CN(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 17, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 30, 45, 45, 41, 45, 45, 45, 45, 45, 45, 32, 32, 32, 32, 32, 32, 17, 17, 3, 3, 1, 3, 45, 45, 41, 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]) total number of confs: 171 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001448072498 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498 Building ZINC001448072498 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448072498 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 756) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(C(F)(F)F)c1) `ZINC001448072498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448072498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001448072498 none CN(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 30, 13, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 46, 46, 37, 46, 46, 46, 46, 46, 46, 30, 30, 30, 30, 30, 30, 13, 13, 4, 3, 1, 3, 46, 46, 37, 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]) total number of confs: 186 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 757) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(C(F)(F)F)c1) `ZINC001448072498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448072498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001448072498 none CN(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 17, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 30, 45, 45, 41, 45, 45, 45, 45, 45, 45, 32, 32, 32, 32, 32, 32, 17, 17, 3, 3, 1, 3, 45, 45, 41, 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]) total number of confs: 171 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001448072498 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072498 Building ZINC001448072504 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448072504 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/758 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(C(F)(F)F)c1) `ZINC001448072504.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448072504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001448072504 none CN(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 30, 16, 28, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 45, 45, 41, 45, 45, 45, 45, 45, 45, 30, 30, 30, 30, 30, 30, 16, 16, 3, 3, 1, 3, 45, 45, 41, 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]) total number of confs: 163 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/759 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/759' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(C(F)(F)F)c1) `ZINC001448072504.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448072504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001448072504 none CN(C)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 29, 12, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 46, 46, 38, 46, 46, 46, 46, 46, 46, 29, 29, 29, 29, 29, 29, 12, 12, 4, 3, 1, 3, 46, 46, 38, 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]) total number of confs: 180 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001448072504 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504 Building ZINC001448072504 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448072504 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 758) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(C(F)(F)F)c1) `ZINC001448072504.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448072504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001448072504 none CN(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 30, 16, 28, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 45, 45, 41, 45, 45, 45, 45, 45, 45, 30, 30, 30, 30, 30, 30, 16, 16, 3, 3, 1, 3, 45, 45, 41, 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]) total number of confs: 163 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 759) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(C)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(C(F)(F)F)c1) `ZINC001448072504.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448072504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001448072504 none CN(C)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 29, 12, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 46, 46, 38, 46, 46, 46, 46, 46, 46, 29, 29, 29, 29, 29, 29, 12, 12, 4, 3, 1, 3, 46, 46, 38, 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]) total number of confs: 180 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001448072504 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448072504 Building ZINC001448418715 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448418715 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/760 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2cccc(F)c2)c(Br)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001448418715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448418715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001448418715 none O=C(Nc1ccc(Oc2cccc(F)c2)c(Br)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 17, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 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, 1, 2, 2, 10, 10, 8, 8, 30, 50, 50, 50, 50, 50, 50, 10, 10, 10, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 50, 50, 50, 50, 10, 2, 2, 4, 2, 2] 100 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/761 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/761' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2cccc(F)c2)c(Br)c1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001448418715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448418715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001448418715 none O=C(Nc1ccc(Oc2cccc(F)c2)c(Br)c1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 17, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 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, 1, 2, 2, 10, 10, 8, 10, 30, 50, 50, 50, 50, 50, 50, 10, 10, 10, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 50, 50, 50, 50, 10, 2, 2, 4, 2, 2] 100 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001448418715 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715 Building ZINC001448418715 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448418715 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 760) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Oc2cccc(F)c2)c(Br)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001448418715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448418715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001448418715 none O=C(Nc1ccc(Oc2cccc(F)c2)c(Br)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 17, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 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, 1, 2, 2, 10, 10, 8, 8, 30, 50, 50, 50, 50, 50, 50, 10, 10, 10, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 50, 50, 50, 50, 10, 2, 2, 4, 2, 2] 100 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 761) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Oc2cccc(F)c2)c(Br)c1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001448418715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448418715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001448418715 none O=C(Nc1ccc(Oc2cccc(F)c2)c(Br)c1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 17, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 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, 1, 2, 2, 10, 10, 8, 10, 30, 50, 50, 50, 50, 50, 50, 10, 10, 10, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 50, 50, 50, 50, 10, 2, 2, 4, 2, 2] 100 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001448418715 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448418715 Building ZINC001448432050 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448432050 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/762 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2ccc(Br)cc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001448432050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448432050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001448432050 none O=C(N1CCC(c2ccc(Br)cc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 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] 0 hydrogens 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, 11, 20, 20, 20, 20, 24, 24, 24, 24, 24, 24, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 24, 24, 24, 24, 20, 20, 20, 20, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 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]) total number of confs: 46 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/763 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/763' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2ccc(Br)cc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001448432050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448432050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001448432050 none O=C(N1CCC(c2ccc(Br)cc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 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] 0 hydrogens 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, 11, 18, 18, 18, 18, 23, 23, 23, 23, 23, 23, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 23, 23, 23, 23, 18, 18, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001448432050 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050 Building ZINC001448432050 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448432050 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 762) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCC(c2ccc(Br)cc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001448432050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448432050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001448432050 none O=C(N1CCC(c2ccc(Br)cc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 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] 0 hydrogens 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, 11, 20, 20, 20, 20, 24, 24, 24, 24, 24, 24, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 24, 24, 24, 24, 20, 20, 20, 20, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 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]) total number of confs: 46 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 763) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCC(c2ccc(Br)cc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001448432050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448432050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001448432050 none O=C(N1CCC(c2ccc(Br)cc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 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] 0 hydrogens 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, 11, 18, 18, 18, 18, 23, 23, 23, 23, 23, 23, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 23, 23, 23, 23, 18, 18, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001448432050 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448432050 Building ZINC001448511945 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448511945 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/764 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H](c2cccc(C(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001448511945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448511945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001448511945 none O=C(N[C@H]1C[C@H](c2cccc(C(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 10, 10, 10, 48, 48, 48, 48, 48, 48, 48, 48, 48, 10, 1, 1, 1, 4, 4, 4, 4, 4, 2, 10, 10, 48, 48, 48, 48, 10, 10, 4, 4] 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/765 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/765' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H](c2cccc(C(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001448511945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448511945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001448511945 none O=C(N[C@H]1C[C@H](c2cccc(C(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 10, 10, 10, 49, 49, 35, 49, 49, 49, 49, 49, 49, 10, 1, 1, 1, 4, 4, 4, 4, 4, 2, 10, 10, 49, 49, 35, 49, 10, 10, 4, 4] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001448511945 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945 Building ZINC001448511945 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448511945 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 764) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@H]1C[C@H](c2cccc(C(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001448511945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448511945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001448511945 none O=C(N[C@H]1C[C@H](c2cccc(C(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 10, 10, 10, 48, 48, 48, 48, 48, 48, 48, 48, 48, 10, 1, 1, 1, 4, 4, 4, 4, 4, 2, 10, 10, 48, 48, 48, 48, 10, 10, 4, 4] 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 765) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@H]1C[C@H](c2cccc(C(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001448511945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448511945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001448511945 none O=C(N[C@H]1C[C@H](c2cccc(C(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 10, 10, 10, 49, 49, 35, 49, 49, 49, 49, 49, 49, 10, 1, 1, 1, 4, 4, 4, 4, 4, 2, 10, 10, 49, 49, 35, 49, 10, 10, 4, 4] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001448511945 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001448511945 Building ZINC001449038821 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449038821 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/766 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O)(c2ccccc2C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001449038821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449038821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001449038821 none O=C(N1CCC(O)(c2ccccc2C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 6, 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, 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] 1 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 19, 33, 33, 33, 33, 33, 36, 36, 34, 36, 36, 36, 36, 36, 36, 33, 33, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 33, 33, 33, 33, 99, 36, 36, 33, 36, 33, 33, 33, 33, 4, 1, 4] 120 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]) total number of confs: 173 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/767 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/767' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O)(c2ccccc2C(F)(F)F)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001449038821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449038821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001449038821 none O=C(N1CCC(O)(c2ccccc2C(F)(F)F)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 6, 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, 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] 1 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 20, 38, 38, 38, 38, 38, 42, 42, 38, 42, 42, 42, 42, 42, 42, 38, 38, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 38, 38, 38, 38, 114, 42, 42, 38, 42, 38, 38, 38, 38, 5, 5, 5] 144 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]) total number of confs: 200 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001449038821 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821 Building ZINC001449038821 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449038821 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 766) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCC(O)(c2ccccc2C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001449038821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449038821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001449038821 none O=C(N1CCC(O)(c2ccccc2C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 6, 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, 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] 1 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 19, 33, 33, 33, 33, 33, 36, 36, 34, 36, 36, 36, 36, 36, 36, 33, 33, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 33, 33, 33, 33, 99, 36, 36, 33, 36, 33, 33, 33, 33, 4, 1, 4] 120 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]) total number of confs: 173 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 767) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCC(O)(c2ccccc2C(F)(F)F)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001449038821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449038821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001449038821 none O=C(N1CCC(O)(c2ccccc2C(F)(F)F)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 6, 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, 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] 1 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 20, 38, 38, 38, 38, 38, 42, 42, 38, 42, 42, 42, 42, 42, 42, 38, 38, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 38, 38, 38, 38, 114, 42, 42, 38, 42, 38, 38, 38, 38, 5, 5, 5] 144 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]) total number of confs: 200 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001449038821 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449038821 Building ZINC001449211825 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449211825 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/768 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCCN(CC1CCCC1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001449211825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449211825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001449211825 none CC(C)(C)OC(=O)NCCCN(CC1CCCC1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', '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, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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: [25, 25, 25, 25, 25, 21, 25, 6, 6, 6, 3, 2, 3, 6, 9, 9, 9, 9, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 25, 21, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/769 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/769' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCCN(CC1CCCC1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001449211825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449211825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001449211825 none CC(C)(C)OC(=O)NCCCN(CC1CCCC1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', '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, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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: [27, 27, 27, 27, 27, 22, 27, 6, 6, 6, 3, 2, 3, 6, 9, 9, 9, 9, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 22, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001449211825 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825 Building ZINC001449211825 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449211825 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 768) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)OC(=O)NCCCN(CC1CCCC1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001449211825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449211825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001449211825 none CC(C)(C)OC(=O)NCCCN(CC1CCCC1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', '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, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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: [25, 25, 25, 25, 25, 21, 25, 6, 6, 6, 3, 2, 3, 6, 9, 9, 9, 9, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 25, 21, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 769) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)OC(=O)NCCCN(CC1CCCC1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001449211825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449211825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001449211825 none CC(C)(C)OC(=O)NCCCN(CC1CCCC1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', '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, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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: [27, 27, 27, 27, 27, 22, 27, 6, 6, 6, 3, 2, 3, 6, 9, 9, 9, 9, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 22, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001449211825 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449211825 Building ZINC001449840749 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449840749 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/770 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCO)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2nc1C(F)(F)F) `ZINC001449840749.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449840749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001449840749 none C[C@H](CCO)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.pl3', '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', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 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: [16, 16, 16, 16, 27, 35, 16, 16, 16, 16, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 27, 27, 35, 35, 105, 16, 16, 4, 8, 8, 16] 150 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]) total number of confs: 251 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/771 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/771' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCO)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2nc1C(F)(F)F) `ZINC001449840749.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449840749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001449840749 none C[C@H](CCO)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.pl3', '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', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 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, 14, 14, 14, 23, 30, 14, 14, 14, 14, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 23, 23, 30, 30, 90, 14, 14, 3, 8, 8, 14] 150 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]) total number of confs: 214 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001449840749 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749 Building ZINC001449840749 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449840749 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 770) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@H](CCO)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2nc1C(F)(F)F) `ZINC001449840749.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449840749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001449840749 none C[C@H](CCO)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.pl3', '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', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 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: [16, 16, 16, 16, 27, 35, 16, 16, 16, 16, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 27, 27, 35, 35, 105, 16, 16, 4, 8, 8, 16] 150 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]) total number of confs: 251 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 771) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@H](CCO)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2nc1C(F)(F)F) `ZINC001449840749.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449840749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001449840749 none C[C@H](CCO)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.pl3', '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', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 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, 14, 14, 14, 23, 30, 14, 14, 14, 14, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 23, 23, 30, 30, 90, 14, 14, 3, 8, 8, 14] 150 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]) total number of confs: 214 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001449840749 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840749 Building ZINC001449840761 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449840761 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/772 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCO)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2nc1C(F)(F)F) `ZINC001449840761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449840761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001449840761 none C[C@@H](CCO)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.pl3', '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', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 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, 14, 14, 14, 23, 31, 14, 14, 14, 14, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 23, 23, 31, 31, 93, 14, 14, 3, 8, 8, 14] 150 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]) total number of confs: 223 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/773 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/773' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCO)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2nc1C(F)(F)F) `ZINC001449840761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449840761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001449840761 none C[C@@H](CCO)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.pl3', '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', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 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: [16, 16, 16, 16, 27, 35, 16, 16, 16, 16, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 27, 27, 35, 35, 105, 16, 16, 4, 8, 8, 16] 150 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]) total number of confs: 251 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001449840761 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761 Building ZINC001449840761 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449840761 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 772) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@H](CCO)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2nc1C(F)(F)F) `ZINC001449840761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449840761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001449840761 none C[C@@H](CCO)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.pl3', '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', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 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, 14, 14, 14, 23, 31, 14, 14, 14, 14, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 23, 23, 31, 31, 93, 14, 14, 3, 8, 8, 14] 150 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]) total number of confs: 223 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 773) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@H](CCO)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2nc1C(F)(F)F) `ZINC001449840761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449840761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001449840761 none C[C@@H](CCO)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.pl3', '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', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 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: [16, 16, 16, 16, 27, 35, 16, 16, 16, 16, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 27, 27, 35, 35, 105, 16, 16, 4, 8, 8, 16] 150 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]) total number of confs: 251 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001449840761 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001449840761 Building ZINC001450736266 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001450736266 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/774 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2c[nH]c3ccc(F)cc32)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001450736266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450736266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001450736266 none O=C(N1CCC(c2c[nH]c3ccc(F)cc32)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 8, 6, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 8, 11, 11, 11, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11, 11, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 32, 32, 32, 32, 11, 11, 11, 11, 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]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/775 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/775' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2c[nH]c3ccc(F)cc32)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001450736266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450736266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001450736266 none O=C(N1CCC(c2c[nH]c3ccc(F)cc32)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 8, 6, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 7, 12, 12, 12, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 12, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 34, 34, 34, 34, 12, 12, 12, 12, 5, 5] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001450736266 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266 Building ZINC001450736266 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001450736266 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 774) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCC(c2c[nH]c3ccc(F)cc32)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001450736266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450736266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001450736266 none O=C(N1CCC(c2c[nH]c3ccc(F)cc32)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 8, 6, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 8, 11, 11, 11, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11, 11, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 32, 32, 32, 32, 11, 11, 11, 11, 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]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 775) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N1CCC(c2c[nH]c3ccc(F)cc32)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001450736266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450736266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001450736266 none O=C(N1CCC(c2c[nH]c3ccc(F)cc32)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 8, 6, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 7, 12, 12, 12, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 12, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 34, 34, 34, 34, 12, 12, 12, 12, 5, 5] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001450736266 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001450736266 Building ZINC001452099036 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452099036 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/776 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(SCCN2CCCCC2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001452099036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452099036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001452099036 none O=C(Nc1ccc(SCCN2CCCCC2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 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] 0 hydrogens need 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, 7, 7, 6, 7, 16, 16, 16, 28, 28, 28, 28, 28, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 16, 16, 16, 16, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7, 4, 4, 4, 4] 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: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/777 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/777' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(SCCN2CCCCC2)cc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001452099036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452099036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001452099036 none O=C(Nc1ccc(SCCN2CCCCC2)cc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 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] 0 hydrogens need 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, 7, 7, 6, 7, 16, 16, 16, 28, 28, 28, 28, 28, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 16, 16, 16, 16, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7, 4, 4, 4, 4] 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: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001452099036 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036 Building ZINC001452099036 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452099036 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 776) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1ccc(SCCN2CCCCC2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001452099036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452099036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001452099036 none O=C(Nc1ccc(SCCN2CCCCC2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 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] 0 hydrogens need 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, 7, 7, 6, 7, 16, 16, 16, 28, 28, 28, 28, 28, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 16, 16, 16, 16, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7, 4, 4, 4, 4] 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: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 777) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1ccc(SCCN2CCCCC2)cc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001452099036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452099036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001452099036 none O=C(Nc1ccc(SCCN2CCCCC2)cc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 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] 0 hydrogens need 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, 7, 7, 6, 7, 16, 16, 16, 28, 28, 28, 28, 28, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 16, 16, 16, 16, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7, 4, 4, 4, 4] 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: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001452099036 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452099036 Building ZINC001452778796 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452778796 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/778 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nn1c1cccc(C(F)(F)F)c1) `ZINC001452778796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452778796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001452778796 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nn1c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 6, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 27, 27, 14, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 3, 5, 5, 5, 5, 27, 27, 27, 27] 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/779 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/779' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nn1c1cccc(C(F)(F)F)c1) `ZINC001452778796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452778796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001452778796 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nn1c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 6, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 26, 26, 14, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 3, 5, 5, 5, 5, 26, 26, 26, 26] 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001452778796 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796 Building ZINC001452778796 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452778796 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 778) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nn1c1cccc(C(F)(F)F)c1) `ZINC001452778796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452778796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001452778796 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nn1c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 6, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 27, 27, 14, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 3, 5, 5, 5, 5, 27, 27, 27, 27] 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 779) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nn1c1cccc(C(F)(F)F)c1) `ZINC001452778796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452778796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001452778796 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nn1c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 6, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 26, 26, 14, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 3, 5, 5, 5, 5, 26, 26, 26, 26] 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001452778796 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001452778796 Building ZINC001453291884 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453291884 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/780 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)Cc2ccccc21) `ZINC001453291884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453291884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001453291884 none CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 40, 8, 40, 8, 8, 8, 6, 1, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 49, 49, 49, 49, 49, 49, 49, 49, 49, 8, 8, 3, 1, 3, 8, 8, 8, 8, 8, 8] 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: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/781 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/781' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)Cc2ccccc21) `ZINC001453291884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453291884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001453291884 none CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 39, 7, 39, 7, 7, 7, 5, 1, 5, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 48, 48, 48, 48, 48, 48, 48, 48, 48, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7] 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: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001453291884 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884 Building ZINC001453291884 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453291884 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 780) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)Cc2ccccc21) `ZINC001453291884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453291884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001453291884 none CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 40, 8, 40, 8, 8, 8, 6, 1, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 49, 49, 49, 49, 49, 49, 49, 49, 49, 8, 8, 3, 1, 3, 8, 8, 8, 8, 8, 8] 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: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 781) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)Cc2ccccc21) `ZINC001453291884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453291884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001453291884 none CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 39, 7, 39, 7, 7, 7, 5, 1, 5, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 48, 48, 48, 48, 48, 48, 48, 48, 48, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7] 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: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001453291884 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291884 Building ZINC001453291888 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453291888 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/782 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)Cc2ccccc21) `ZINC001453291888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453291888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001453291888 none CC(C)(C)OC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 39, 7, 39, 7, 7, 7, 5, 1, 5, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 48, 48, 48, 48, 48, 48, 48, 48, 48, 7, 7, 3, 1, 3, 7, 7, 7, 7, 7, 7] 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/783 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/783' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)Cc2ccccc21) `ZINC001453291888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453291888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001453291888 none CC(C)(C)OC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 40, 8, 40, 8, 8, 8, 6, 2, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 49, 49, 49, 49, 49, 49, 49, 49, 49, 8, 8, 3, 1, 3, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 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: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001453291888 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888 Building ZINC001453291888 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453291888 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 782) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)OC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)Cc2ccccc21) `ZINC001453291888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453291888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001453291888 none CC(C)(C)OC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 39, 7, 39, 7, 7, 7, 5, 1, 5, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 48, 48, 48, 48, 48, 48, 48, 48, 48, 7, 7, 3, 1, 3, 7, 7, 7, 7, 7, 7] 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 783) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)OC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)Cc2ccccc21) `ZINC001453291888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453291888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001453291888 none CC(C)(C)OC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 40, 8, 40, 8, 8, 8, 6, 2, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 49, 49, 49, 49, 49, 49, 49, 49, 49, 8, 8, 3, 1, 3, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 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: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001453291888 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001453291888 Building ZINC001454631176 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454631176 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/784 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1c2ccccc2[nH]c1C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001454631176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454631176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001454631176 none O=C(NCCc1c2ccccc2[nH]c1C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 6, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 4, 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] 0 hydrogens 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, 22, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 11, 11, 11, 11, 11, 5, 22, 22, 29, 29, 29, 29, 29, 29, 11, 11] 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]) total number of confs: 124 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/785 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/785' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1c2ccccc2[nH]c1C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001454631176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454631176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001454631176 none O=C(NCCc1c2ccccc2[nH]c1C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 6, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 4, 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] 0 hydrogens 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, 22, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 11, 11, 11, 11, 11, 5, 22, 22, 29, 29, 29, 29, 29, 29, 11, 11] 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]) total number of confs: 124 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001454631176 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176 Building ZINC001454631176 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454631176 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 784) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCCc1c2ccccc2[nH]c1C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001454631176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454631176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001454631176 none O=C(NCCc1c2ccccc2[nH]c1C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 6, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 4, 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] 0 hydrogens 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, 22, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 11, 11, 11, 11, 11, 5, 22, 22, 29, 29, 29, 29, 29, 29, 11, 11] 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]) total number of confs: 124 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 785) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCCc1c2ccccc2[nH]c1C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001454631176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454631176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001454631176 none O=C(NCCc1c2ccccc2[nH]c1C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 6, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 4, 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] 0 hydrogens 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, 22, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 11, 11, 11, 11, 11, 5, 22, 22, 29, 29, 29, 29, 29, 29, 11, 11] 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]) total number of confs: 124 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001454631176 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001454631176 Building ZINC001455151345 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455151345 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/786 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2(CCC2)[C@@H]1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001455151345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455151345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001455151345 none CC(C)(C)OC(=O)N1CC2(CCC2)[C@@H]1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 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, 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, 6, 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] 0 hydrogens 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, 35, 19, 35, 19, 19, 19, 19, 19, 19, 9, 19, 9, 9, 9, 2, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 9, 9, 9, 2, 2, 2, 2, 9, 9, 9, 9] 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, 59, 60, 61]) total number of confs: 138 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/787 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/787' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2(CCC2)[C@@H]1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001455151345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455151345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001455151345 none CC(C)(C)OC(=O)N1CC2(CCC2)[C@@H]1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 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, 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, 6, 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] 0 hydrogens 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, 37, 19, 37, 19, 19, 19, 19, 19, 19, 10, 19, 10, 10, 10, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 10, 10, 10, 1, 1, 1, 1, 10, 10, 10, 10] 50 rigid atoms, others: [54, 57, 55, 56, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 58, 59, 60, 61]) total number of confs: 133 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001455151345 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345 Building ZINC001455151345 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455151345 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 786) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)OC(=O)N1CC2(CCC2)[C@@H]1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001455151345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455151345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001455151345 none CC(C)(C)OC(=O)N1CC2(CCC2)[C@@H]1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 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, 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, 6, 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] 0 hydrogens 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, 35, 19, 35, 19, 19, 19, 19, 19, 19, 9, 19, 9, 9, 9, 2, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 9, 9, 9, 2, 2, 2, 2, 9, 9, 9, 9] 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, 59, 60, 61]) total number of confs: 138 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 787) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)OC(=O)N1CC2(CCC2)[C@@H]1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001455151345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455151345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001455151345 none CC(C)(C)OC(=O)N1CC2(CCC2)[C@@H]1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 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, 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, 6, 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] 0 hydrogens 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, 37, 19, 37, 19, 19, 19, 19, 19, 19, 10, 19, 10, 10, 10, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 10, 10, 10, 1, 1, 1, 1, 10, 10, 10, 10] 50 rigid atoms, others: [54, 57, 55, 56, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 58, 59, 60, 61]) total number of confs: 133 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001455151345 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151345 Building ZINC001455151349 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455151349 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/788 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2(CCC2)[C@H]1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001455151349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455151349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001455151349 none CC(C)(C)OC(=O)N1CC2(CCC2)[C@H]1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 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, 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, 6, 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] 0 hydrogens 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, 42, 21, 42, 21, 21, 21, 21, 21, 21, 10, 21, 10, 10, 10, 2, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 3, 3, 3, 3, 10, 10, 10, 10] 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, 59, 60, 61]) total number of confs: 146 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/789 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/789' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2(CCC2)[C@H]1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001455151349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455151349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001455151349 none CC(C)(C)OC(=O)N1CC2(CCC2)[C@H]1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 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, 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, 6, 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] 0 hydrogens 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, 36, 20, 36, 20, 20, 20, 20, 20, 20, 7, 20, 7, 7, 7, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [54, 57, 55, 56, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 58, 59, 60, 61]) total number of confs: 133 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001455151349 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349 Building ZINC001455151349 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455151349 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 788) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)OC(=O)N1CC2(CCC2)[C@H]1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001455151349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455151349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001455151349 none CC(C)(C)OC(=O)N1CC2(CCC2)[C@H]1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 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, 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, 6, 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] 0 hydrogens 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, 42, 21, 42, 21, 21, 21, 21, 21, 21, 10, 21, 10, 10, 10, 2, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 3, 3, 3, 3, 10, 10, 10, 10] 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, 59, 60, 61]) total number of confs: 146 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 789) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)OC(=O)N1CC2(CCC2)[C@H]1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001455151349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455151349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001455151349 none CC(C)(C)OC(=O)N1CC2(CCC2)[C@H]1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 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, 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, 6, 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] 0 hydrogens 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, 36, 20, 36, 20, 20, 20, 20, 20, 20, 7, 20, 7, 7, 7, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [54, 57, 55, 56, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 58, 59, 60, 61]) total number of confs: 133 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001455151349 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455151349 Building ZINC001455302995 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455302995 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/790 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(F)ccc1Oc1ccc(Cl)c(F)c1)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001455302995.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455302995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001455302995 none CN(Cc1cc(F)ccc1Oc1ccc(Cl)c(F)c1)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 8, 5, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 15, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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: [3, 2, 3, 8, 13, 13, 13, 13, 13, 13, 13, 27, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 13, 8, 13, 50, 50, 50, 1, 1, 2, 1, 1] 100 rigid atoms, others: [41, 42, 44, 45, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/182395/xbh-8058088.34/working/building/ZINC001455302995 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/791 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/791' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(F)ccc1Oc1ccc(Cl)c(F)c1)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001455302995.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455302995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001455302995 none CN(Cc1cc(F)ccc1Oc1ccc(Cl)c(F)c1)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 8, 5, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 15, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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: [4, 2, 4, 9, 14, 14, 14, 14, 14, 14, 14, 27, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 14, 9, 14, 50, 50, 50, 1, 1, 2, 1, 1] 100 rigid atoms, others: [41, 42, 44, 45, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001455302995 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995 Building ZINC001455302995 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455302995 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 790) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(Cc1cc(F)ccc1Oc1ccc(Cl)c(F)c1)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001455302995.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455302995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001455302995 none CN(Cc1cc(F)ccc1Oc1ccc(Cl)c(F)c1)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 8, 5, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 15, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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: [3, 2, 3, 8, 13, 13, 13, 13, 13, 13, 13, 27, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 13, 8, 13, 50, 50, 50, 1, 1, 2, 1, 1] 100 rigid atoms, others: [41, 42, 44, 45, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/182395/xbh-8058088.34/working/building/ZINC001455302995 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 791) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(Cc1cc(F)ccc1Oc1ccc(Cl)c(F)c1)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001455302995.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455302995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001455302995 none CN(Cc1cc(F)ccc1Oc1ccc(Cl)c(F)c1)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 8, 5, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 15, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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: [4, 2, 4, 9, 14, 14, 14, 14, 14, 14, 14, 27, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 14, 9, 14, 50, 50, 50, 1, 1, 2, 1, 1] 100 rigid atoms, others: [41, 42, 44, 45, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001455302995 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455302995 Building ZINC001455937245 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455937245 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/792 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCN(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1) `ZINC001455937245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455937245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001455937245 none COc1ccc(CCN(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)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.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 4, 2, 4, 9, 10, 10, 9, 10, 10, 1, 2, 1, 1, 1, 6, 6, 2, 6, 14, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 9, 9, 10, 10, 10, 10, 10, 6, 6, 14, 14, 14, 6, 10, 10] 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: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/793 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/793' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCN(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1) `ZINC001455937245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455937245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001455937245 none COc1ccc(CCN(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)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.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 4, 2, 4, 9, 10, 10, 9, 10, 10, 1, 2, 1, 1, 1, 6, 6, 2, 6, 14, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 9, 9, 10, 10, 9, 10, 10, 6, 6, 14, 14, 14, 6, 10, 10] 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: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001455937245 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245 Building ZINC001455937245 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455937245 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 792) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc(CCN(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1) `ZINC001455937245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455937245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001455937245 none COc1ccc(CCN(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)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.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 4, 2, 4, 9, 10, 10, 9, 10, 10, 1, 2, 1, 1, 1, 6, 6, 2, 6, 14, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 9, 9, 10, 10, 10, 10, 10, 6, 6, 14, 14, 14, 6, 10, 10] 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: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 793) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc(CCN(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1) `ZINC001455937245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455937245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001455937245 none COc1ccc(CCN(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)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.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 4, 2, 4, 9, 10, 10, 9, 10, 10, 1, 2, 1, 1, 1, 6, 6, 2, 6, 14, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 9, 9, 10, 10, 9, 10, 10, 6, 6, 14, 14, 14, 6, 10, 10] 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: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001455937245 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001455937245 Building ZINC001456021042 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456021042 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/794 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C(=O)OCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001456021042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456021042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001456021042 none O=C(Nc1cccc(C(=O)OCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 7, 5, 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] 0 hydrogens need 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, 8, 8, 21, 21, 22, 41, 48, 48, 41, 48, 48, 8, 1, 1, 1, 5, 5, 5, 5, 5, 2, 8, 8, 8, 41, 41, 48, 48, 41, 48, 48, 8, 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/795 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/795' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C(=O)OCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001456021042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456021042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001456021042 none O=C(Nc1cccc(C(=O)OCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 7, 5, 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] 0 hydrogens need 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, 8, 8, 20, 20, 21, 40, 48, 48, 40, 48, 48, 8, 1, 1, 1, 5, 5, 5, 5, 5, 2, 8, 8, 8, 40, 40, 48, 48, 40, 48, 48, 8, 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456021042 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042 Building ZINC001456021042 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456021042 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 794) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cccc(C(=O)OCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001456021042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456021042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001456021042 none O=C(Nc1cccc(C(=O)OCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 7, 5, 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] 0 hydrogens need 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, 8, 8, 21, 21, 22, 41, 48, 48, 41, 48, 48, 8, 1, 1, 1, 5, 5, 5, 5, 5, 2, 8, 8, 8, 41, 41, 48, 48, 41, 48, 48, 8, 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 795) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1cccc(C(=O)OCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001456021042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456021042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001456021042 none O=C(Nc1cccc(C(=O)OCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 7, 5, 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] 0 hydrogens need 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, 8, 8, 20, 20, 21, 40, 48, 48, 40, 48, 48, 8, 1, 1, 1, 5, 5, 5, 5, 5, 2, 8, 8, 8, 40, 40, 48, 48, 40, 48, 48, 8, 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456021042 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456021042 Building ZINC001456090590 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456090590 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/796 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccc2c(c1)OCO2)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001456090590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456090590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001456090590 none O=C(N(Cc1ccc2c(c1)OCO2)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 3, 7, 3, 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] 0 hydrogens 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, 8, 15, 32, 32, 32, 32, 32, 32, 32, 32, 8, 11, 11, 8, 11, 11, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 32, 32, 32, 32, 32, 11, 11, 8, 11, 11, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/797 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/797' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccc2c(c1)OCO2)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001456090590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456090590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001456090590 none O=C(N(Cc1ccc2c(c1)OCO2)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1 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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 3, 7, 3, 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] 0 hydrogens 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, 7, 14, 31, 31, 31, 31, 31, 31, 31, 31, 7, 9, 9, 9, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 14, 14, 31, 31, 31, 31, 31, 9, 9, 9, 9, 9, 4, 4] 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456090590 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590 Building ZINC001456090590 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456090590 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 796) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N(Cc1ccc2c(c1)OCO2)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001456090590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456090590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001456090590 none O=C(N(Cc1ccc2c(c1)OCO2)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 3, 7, 3, 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] 0 hydrogens 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, 8, 15, 32, 32, 32, 32, 32, 32, 32, 32, 8, 11, 11, 8, 11, 11, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 32, 32, 32, 32, 32, 11, 11, 8, 11, 11, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 797) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N(Cc1ccc2c(c1)OCO2)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001456090590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456090590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001456090590 none O=C(N(Cc1ccc2c(c1)OCO2)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1 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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 3, 7, 3, 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] 0 hydrogens 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, 7, 14, 31, 31, 31, 31, 31, 31, 31, 31, 7, 9, 9, 9, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 14, 14, 31, 31, 31, 31, 31, 9, 9, 9, 9, 9, 4, 4] 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456090590 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456090590 Building ZINC001456142142 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456142142 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/798 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(Br)cc1CN(C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)C1CC1) `ZINC001456142142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456142142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001456142142 none CCOc1ccc(Br)cc1CN(C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', '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, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 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] dock color type numbers: [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] 0 hydrogens 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, 45, 23, 23, 23, 18, 23, 23, 23, 14, 7, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 7, 11, 11, 47, 47, 47, 47, 47, 23, 23, 23, 14, 14, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11] 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]) total number of confs: 159 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/799 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/799' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(Br)cc1CN(C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)C1CC1) `ZINC001456142142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456142142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001456142142 none CCOc1ccc(Br)cc1CN(C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', '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, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 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] dock color type numbers: [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] 0 hydrogens 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, 24, 24, 24, 18, 24, 24, 24, 18, 8, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 14, 14, 50, 50, 50, 50, 50, 24, 24, 24, 18, 18, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14] 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]) total number of confs: 194 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456142142 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142 Building ZINC001456142142 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456142142 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 798) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCOc1ccc(Br)cc1CN(C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)C1CC1) `ZINC001456142142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456142142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001456142142 none CCOc1ccc(Br)cc1CN(C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', '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, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 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] dock color type numbers: [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] 0 hydrogens 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, 45, 23, 23, 23, 18, 23, 23, 23, 14, 7, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 7, 11, 11, 47, 47, 47, 47, 47, 23, 23, 23, 14, 14, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11] 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]) total number of confs: 159 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 799) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCOc1ccc(Br)cc1CN(C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)C1CC1) `ZINC001456142142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456142142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001456142142 none CCOc1ccc(Br)cc1CN(C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', '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, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 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] dock color type numbers: [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] 0 hydrogens 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, 24, 24, 24, 18, 24, 24, 24, 18, 8, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 14, 14, 50, 50, 50, 50, 50, 24, 24, 24, 18, 18, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14] 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]) total number of confs: 194 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456142142 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456142142 Building ZINC001456150479 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456150479 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/800 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)OC(C)(C)C)cc1C(F)(F)F) `ZINC001456150479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456150479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001456150479 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)OC(C)(C)C)cc1C(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', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations 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, 3, 3, 3, 5, 5, 3, 5, 28, 43, 43, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 3, 5, 5, 28, 50, 50, 50, 50, 50, 48, 50, 50, 50, 5] 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/801 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/801' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)OC(C)(C)C)cc1C(F)(F)F) `ZINC001456150479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456150479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001456150479 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)OC(C)(C)C)cc1C(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', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations 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, 3, 3, 3, 5, 5, 3, 5, 24, 40, 41, 50, 50, 49, 50, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 3, 5, 5, 26, 50, 49, 50, 50, 49, 46, 50, 49, 50, 5] 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456150479 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479 Building ZINC001456150479 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456150479 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 800) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)OC(C)(C)C)cc1C(F)(F)F) `ZINC001456150479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456150479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001456150479 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)OC(C)(C)C)cc1C(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', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations 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, 3, 3, 3, 5, 5, 3, 5, 28, 43, 43, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 3, 5, 5, 28, 50, 50, 50, 50, 50, 48, 50, 50, 50, 5] 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 801) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)OC(C)(C)C)cc1C(F)(F)F) `ZINC001456150479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456150479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001456150479 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)OC(C)(C)C)cc1C(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', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations 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, 3, 3, 3, 5, 5, 3, 5, 24, 40, 41, 50, 50, 49, 50, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 3, 5, 5, 26, 50, 49, 50, 50, 49, 46, 50, 49, 50, 5] 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456150479 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456150479 Building ZINC001456170528 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456170528 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/802 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(Sc2ccc(N3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(O)cc4)CC3)cc2)c(C)c1) `ZINC001456170528.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456170528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001456170528 none Cc1ccc(Sc2ccc(N3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(O)cc4)CC3)cc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 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: [43, 46, 46, 50, 34, 4, 4, 15, 15, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 4, 4, 4, 4, 1, 1, 2, 1, 1, 4, 4, 4, 4, 15, 15, 50, 50, 50, 50] 100 rigid atoms, others: [43, 44, 46, 47, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/803 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/803' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(Sc2ccc(N3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(O)cc4)CC3)cc2)c(C)c1) `ZINC001456170528.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456170528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001456170528 none Cc1ccc(Sc2ccc(N3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(O)cc4)CC3)cc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 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: [46, 46, 50, 50, 27, 4, 4, 15, 15, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 4, 4, 4, 4, 1, 1, 2, 1, 1, 4, 4, 4, 4, 15, 15, 50, 50, 50, 50] 100 rigid atoms, others: [43, 44, 46, 47, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456170528 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528 Building ZINC001456170528 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456170528 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 802) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(Sc2ccc(N3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(O)cc4)CC3)cc2)c(C)c1) `ZINC001456170528.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456170528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001456170528 none Cc1ccc(Sc2ccc(N3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(O)cc4)CC3)cc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 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: [43, 46, 46, 50, 34, 4, 4, 15, 15, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 4, 4, 4, 4, 1, 1, 2, 1, 1, 4, 4, 4, 4, 15, 15, 50, 50, 50, 50] 100 rigid atoms, others: [43, 44, 46, 47, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 803) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(Sc2ccc(N3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(O)cc4)CC3)cc2)c(C)c1) `ZINC001456170528.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456170528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001456170528 none Cc1ccc(Sc2ccc(N3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(O)cc4)CC3)cc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 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: [46, 46, 50, 50, 27, 4, 4, 15, 15, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 4, 4, 4, 4, 1, 1, 2, 1, 1, 4, 4, 4, 4, 15, 15, 50, 50, 50, 50] 100 rigid atoms, others: [43, 44, 46, 47, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456170528 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456170528 Building ZINC001456201252 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456201252 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/804 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1cccc(OCCCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001456201252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456201252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001456201252 none O=C(NCCc1cccc(OCCCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', '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', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 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, 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, 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] 0 hydrogens need 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, 7, 8, 9, 9, 9, 9, 9, 11, 15, 29, 29, 29, 29, 29, 29, 29, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 7, 7, 8, 8, 9, 9, 9, 15, 15, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6] 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, 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/182395/xbh-8058088.34/working/building/ZINC001456201252 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/805 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/805' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1cccc(OCCCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001456201252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456201252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001456201252 none O=C(NCCc1cccc(OCCCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', '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', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 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, 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, 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] 0 hydrogens need 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, 7, 8, 9, 9, 9, 9, 9, 11, 15, 28, 28, 28, 28, 28, 28, 28, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 7, 7, 8, 8, 9, 9, 9, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6] 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, 60]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456201252 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252 Building ZINC001456201252 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456201252 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 804) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCCc1cccc(OCCCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001456201252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456201252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001456201252 none O=C(NCCc1cccc(OCCCc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', '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', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 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, 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, 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] 0 hydrogens need 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, 7, 8, 9, 9, 9, 9, 9, 11, 15, 29, 29, 29, 29, 29, 29, 29, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 7, 7, 8, 8, 9, 9, 9, 15, 15, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6] 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, 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/182395/xbh-8058088.34/working/building/ZINC001456201252 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 805) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCCc1cccc(OCCCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001456201252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456201252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001456201252 none O=C(NCCc1cccc(OCCCc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', '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', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 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, 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, 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] 0 hydrogens need 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, 7, 8, 9, 9, 9, 9, 9, 11, 15, 28, 28, 28, 28, 28, 28, 28, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 7, 7, 8, 8, 9, 9, 9, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6] 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, 60]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456201252 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456201252 Building ZINC001456299891 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456299891 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/806 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1Cc1ccc(Cl)c(F)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456299891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456299891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001456299891 none O=C(Nc1ccnn1Cc1ccc(Cl)c(F)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 15, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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] 0 hydrogens need 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, 5, 12, 12, 12, 12, 12, 30, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 5, 12, 12, 30, 30, 48, 48, 48, 3, 1, 3] 50 rigid atoms, others: [1, 17, 18, 19] 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/807 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/807' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1Cc1ccc(Cl)c(F)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456299891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456299891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001456299891 none O=C(Nc1ccnn1Cc1ccc(Cl)c(F)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 15, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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] 0 hydrogens need 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, 5, 12, 12, 12, 12, 12, 30, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 5, 12, 12, 30, 30, 48, 48, 48, 3, 1, 3] 50 rigid atoms, others: [1, 17, 18, 19] 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]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456299891 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891 Building ZINC001456299891 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456299891 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 806) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1ccnn1Cc1ccc(Cl)c(F)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456299891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456299891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001456299891 none O=C(Nc1ccnn1Cc1ccc(Cl)c(F)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 15, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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] 0 hydrogens need 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, 5, 12, 12, 12, 12, 12, 30, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 5, 12, 12, 30, 30, 48, 48, 48, 3, 1, 3] 50 rigid atoms, others: [1, 17, 18, 19] 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 807) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1ccnn1Cc1ccc(Cl)c(F)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456299891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456299891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001456299891 none O=C(Nc1ccnn1Cc1ccc(Cl)c(F)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 15, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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] 0 hydrogens need 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, 5, 12, 12, 12, 12, 12, 30, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 5, 12, 12, 30, 30, 48, 48, 48, 3, 1, 3] 50 rigid atoms, others: [1, 17, 18, 19] 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]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456299891 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456299891 Building ZINC001456305559 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456305559 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/808 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Cc1ccc(Cl)cc1Cl) `ZINC001456305559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456305559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001456305559 none CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Cc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 29, 13, 26, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 24, 34, 38, 38, 38, 38, 38, 38, 38, 29, 29, 29, 29, 29, 29, 29, 13, 13, 2, 5, 5, 5, 5, 5, 5, 5, 34, 33, 38, 38, 38] 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/809 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/809' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Cc1ccc(Cl)cc1Cl) `ZINC001456305559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456305559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001456305559 none CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Cc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 31, 14, 27, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 26, 36, 40, 40, 40, 40, 40, 40, 40, 31, 31, 31, 31, 31, 31, 31, 14, 14, 2, 5, 5, 5, 5, 5, 5, 5, 36, 36, 40, 40, 40] 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]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456305559 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559 Building ZINC001456305559 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456305559 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 808) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Cc1ccc(Cl)cc1Cl) `ZINC001456305559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456305559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001456305559 none CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Cc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 29, 13, 26, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 24, 34, 38, 38, 38, 38, 38, 38, 38, 29, 29, 29, 29, 29, 29, 29, 13, 13, 2, 5, 5, 5, 5, 5, 5, 5, 34, 33, 38, 38, 38] 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 809) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Cc1ccc(Cl)cc1Cl) `ZINC001456305559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456305559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001456305559 none CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Cc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 31, 14, 27, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 26, 36, 40, 40, 40, 40, 40, 40, 40, 31, 31, 31, 31, 31, 31, 31, 14, 14, 2, 5, 5, 5, 5, 5, 5, 5, 36, 36, 40, 40, 40] 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]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456305559 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305559 Building ZINC001456305563 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456305563 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/810 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Cc1ccc(Cl)cc1Cl) `ZINC001456305563.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456305563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001456305563 none CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Cc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 31, 14, 27, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 26, 36, 40, 40, 40, 40, 40, 40, 40, 31, 31, 31, 31, 31, 31, 31, 14, 14, 2, 5, 5, 5, 5, 5, 5, 5, 36, 36, 40, 40, 40] 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]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/811 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/811' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Cc1ccc(Cl)cc1Cl) `ZINC001456305563.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456305563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001456305563 none CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Cc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 31, 13, 27, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 35, 38, 38, 38, 38, 38, 38, 38, 31, 31, 31, 31, 31, 31, 31, 13, 13, 2, 5, 5, 5, 5, 5, 5, 5, 34, 35, 38, 38, 38] 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]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456305563 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563 Building ZINC001456305563 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456305563 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 810) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Cc1ccc(Cl)cc1Cl) `ZINC001456305563.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456305563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001456305563 none CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Cc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 31, 14, 27, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 26, 36, 40, 40, 40, 40, 40, 40, 40, 31, 31, 31, 31, 31, 31, 31, 14, 14, 2, 5, 5, 5, 5, 5, 5, 5, 36, 36, 40, 40, 40] 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]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 811) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Cc1ccc(Cl)cc1Cl) `ZINC001456305563.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456305563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001456305563 none CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Cc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 31, 13, 27, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 35, 38, 38, 38, 38, 38, 38, 38, 31, 31, 31, 31, 31, 31, 31, 13, 13, 2, 5, 5, 5, 5, 5, 5, 5, 34, 35, 38, 38, 38] 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]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456305563 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456305563 Building ZINC001456335832 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456335832 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/812 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)cc1) `ZINC001456335832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456335832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001456335832 none COc1ccc(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', '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.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens 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, 34, 37, 48, 48, 42, 22, 42, 42, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 42, 42, 48, 48, 48, 48, 48, 48, 48, 42, 42, 13, 13, 2, 4, 4, 42, 42, 48, 48] 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]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/813 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/813' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)cc1) `ZINC001456335832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456335832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001456335832 none COc1ccc(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', '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.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens 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, 36, 36, 49, 49, 42, 22, 42, 42, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 42, 42, 49, 49, 49, 49, 49, 49, 49, 42, 42, 13, 13, 2, 4, 4, 42, 42, 49, 49] 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]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456335832 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832 Building ZINC001456335832 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456335832 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 812) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)cc1) `ZINC001456335832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456335832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001456335832 none COc1ccc(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', '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.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens 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, 34, 37, 48, 48, 42, 22, 42, 42, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 42, 42, 48, 48, 48, 48, 48, 48, 48, 42, 42, 13, 13, 2, 4, 4, 42, 42, 48, 48] 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]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 813) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)cc1) `ZINC001456335832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456335832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001456335832 none COc1ccc(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', '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.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens 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, 36, 36, 49, 49, 42, 22, 42, 42, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 42, 42, 49, 49, 49, 49, 49, 49, 49, 42, 42, 13, 13, 2, 4, 4, 42, 42, 49, 49] 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]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456335832 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456335832 Building ZINC001456362866 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456362866 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/814 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)c1) `ZINC001456362866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456362866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001456362866 none COc1cccc(c2ccc(CNC(=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', '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', 'C.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, 1, 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, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 33, 33, 33, 6, 6, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 18, 18, 33, 48, 48, 48, 33, 33, 33, 18, 18, 6, 6, 1, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 18, 18, 33] 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, 57]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/815 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/815' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)c1) `ZINC001456362866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456362866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001456362866 none COc1cccc(c2ccc(CNC(=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', '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', 'C.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, 1, 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, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 18, 18, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 18, 18, 34, 49, 49, 49, 34, 34, 34, 18, 18, 6, 6, 1, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 18, 18, 34] 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, 57]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456362866 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866 Building ZINC001456362866 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456362866 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 814) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1cccc(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)c1) `ZINC001456362866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456362866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001456362866 none COc1cccc(c2ccc(CNC(=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', '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', 'C.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, 1, 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, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 33, 33, 33, 6, 6, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 18, 18, 33, 48, 48, 48, 33, 33, 33, 18, 18, 6, 6, 1, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 18, 18, 33] 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, 57]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 815) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1cccc(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)c1) `ZINC001456362866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456362866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001456362866 none COc1cccc(c2ccc(CNC(=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', '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', 'C.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, 1, 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, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 18, 18, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 18, 18, 34, 49, 49, 49, 34, 34, 34, 18, 18, 6, 6, 1, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 18, 18, 34] 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, 57]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456362866 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456362866 Building ZINC001456442377 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456442377 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/816 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/816' -> `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)(C)c1cccs1) `ZINC001456442377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456442377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001456442377 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'C.2', 'C.2', 'C.2', 'S.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, 1, 1, 1, 1, 14, 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] 0 hydrogens 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, 7, 7, 1, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 14, 14, 14, 14, 1, 1, 1, 7, 7, 1, 7, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 32, 14, 15, 16, 17, 18, 39, 19, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 50 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/817 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/817' -> `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)(C)c1cccs1) `ZINC001456442377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456442377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001456442377 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'C.2', 'C.2', 'C.2', 'S.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, 1, 1, 1, 1, 14, 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] 0 hydrogens 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, 7, 7, 1, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 14, 14, 14, 14, 1, 1, 1, 7, 7, 1, 7, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 32, 14, 15, 16, 17, 18, 39, 19, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 50 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456442377 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377 Building ZINC001456442377 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456442377 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 816) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/816: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)(C)c1cccs1) `ZINC001456442377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456442377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001456442377 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'C.2', 'C.2', 'C.2', 'S.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, 1, 1, 1, 1, 14, 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] 0 hydrogens 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, 7, 7, 1, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 14, 14, 14, 14, 1, 1, 1, 7, 7, 1, 7, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 32, 14, 15, 16, 17, 18, 39, 19, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 50 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 817) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/817: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)(C)c1cccs1) `ZINC001456442377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456442377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001456442377 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'C.2', 'C.2', 'C.2', 'S.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, 1, 1, 1, 1, 14, 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] 0 hydrogens 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, 7, 7, 1, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 14, 14, 14, 14, 1, 1, 1, 7, 7, 1, 7, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 32, 14, 15, 16, 17, 18, 39, 19, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 50 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456442377 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456442377 Building ZINC001456535695 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456535695 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/818 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(Br)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)n1C) `ZINC001456535695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456535695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001456535695 none Cc1nc(c2ccc(Br)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)n1C 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', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.pl3', 'C.3', '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, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 23, 25, 34, 34, 8, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 34, 34, 34, 34, 8, 9, 9, 19, 19, 19] 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: 96 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/819 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/819' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(Br)cc2)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)n1C) `ZINC001456535695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456535695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001456535695 none Cc1nc(c2ccc(Br)cc2)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)n1C 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', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.pl3', 'C.3', '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, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 33, 33, 24, 33, 33, 33, 8, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 33, 33, 33, 33, 8, 9, 9, 18, 18, 18] 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: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456535695 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695 Building ZINC001456535695 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456535695 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 818) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nc(c2ccc(Br)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)n1C) `ZINC001456535695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456535695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001456535695 none Cc1nc(c2ccc(Br)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)n1C 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', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.pl3', 'C.3', '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, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 23, 25, 34, 34, 8, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 34, 34, 34, 34, 8, 9, 9, 19, 19, 19] 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: 96 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 819) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nc(c2ccc(Br)cc2)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)n1C) `ZINC001456535695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456535695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001456535695 none Cc1nc(c2ccc(Br)cc2)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)n1C 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', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.pl3', 'C.3', '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, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 33, 33, 24, 33, 33, 33, 8, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 33, 33, 33, 33, 8, 9, 9, 18, 18, 18] 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: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456535695 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456535695 Building ZINC001456542747 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456542747 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/820 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1) `ZINC001456542747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456542747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001456542747 none Cc1ccc(C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', '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', 'S.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, 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, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 10, 10, 10, 10, 10, 10, 8, 8, 3, 3, 3, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 50 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 42] set([0, 1, 2, 3, 4, 5, 7, 8, 15, 16, 17, 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]) total number of confs: 58 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/821 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/821' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1) `ZINC001456542747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456542747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001456542747 none Cc1ccc(C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', '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', 'S.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, 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, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 13, 13, 13, 13, 13, 13, 7, 7, 3, 3, 3, 1, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 50 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 42] set([0, 1, 2, 3, 4, 5, 7, 8, 15, 16, 17, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456542747 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747 Building ZINC001456542747 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456542747 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 820) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1) `ZINC001456542747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456542747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001456542747 none Cc1ccc(C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', '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', 'S.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, 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, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 10, 10, 10, 10, 10, 10, 8, 8, 3, 3, 3, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 50 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 42] set([0, 1, 2, 3, 4, 5, 7, 8, 15, 16, 17, 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]) total number of confs: 58 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 821) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1) `ZINC001456542747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456542747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001456542747 none Cc1ccc(C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', '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', 'S.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, 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, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 13, 13, 13, 13, 13, 13, 7, 7, 3, 3, 3, 1, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 50 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 42] set([0, 1, 2, 3, 4, 5, 7, 8, 15, 16, 17, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456542747 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542747 Building ZINC001456542777 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456542777 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/822 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1) `ZINC001456542777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456542777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001456542777 none Cc1ccc(C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', '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', 'S.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, 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, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 13, 13, 13, 13, 13, 13, 7, 7, 3, 3, 3, 1, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 50 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 42] set([0, 1, 2, 3, 4, 5, 7, 8, 15, 16, 17, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/823 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/823' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1) `ZINC001456542777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456542777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001456542777 none Cc1ccc(C[C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', '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', 'S.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, 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, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 3, 1, 3, 3, 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, 8, 8, 3, 3, 3, 1, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2] 50 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 42] set([0, 1, 2, 3, 4, 5, 7, 8, 15, 16, 17, 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]) total number of confs: 64 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456542777 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777 Building ZINC001456542777 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456542777 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 822) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1) `ZINC001456542777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456542777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001456542777 none Cc1ccc(C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', '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', 'S.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, 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, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 13, 13, 13, 13, 13, 13, 7, 7, 3, 3, 3, 1, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 50 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 42] set([0, 1, 2, 3, 4, 5, 7, 8, 15, 16, 17, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 823) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(C[C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1) `ZINC001456542777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456542777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001456542777 none Cc1ccc(C[C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', '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', 'S.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, 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, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 3, 1, 3, 3, 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, 8, 8, 3, 3, 3, 1, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2] 50 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 42] set([0, 1, 2, 3, 4, 5, 7, 8, 15, 16, 17, 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]) total number of confs: 64 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456542777 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456542777 Building ZINC001456605783 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456605783 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/824 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(c3ccco3)nn2c2cccc(C)c2)cc1Cl) `ZINC001456605783.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456605783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001456605783 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(c3ccco3)nn2c2cccc(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.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 16, 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, 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] 0 hydrogens 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, 1, 3, 3, 4, 7, 7, 7, 12, 12, 12, 12, 7, 7, 7, 13, 13, 13, 13, 13, 13, 6, 6, 6, 10, 10, 10, 6, 6, 4, 7, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/825 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/825' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3ccco3)nn2c2cccc(C)c2)cc1Cl) `ZINC001456605783.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456605783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001456605783 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3ccco3)nn2c2cccc(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.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 16, 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, 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] 0 hydrogens 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, 1, 2, 2, 3, 6, 6, 6, 11, 11, 11, 11, 6, 6, 6, 12, 12, 6, 12, 12, 12, 6, 6, 6, 10, 10, 10, 6, 6, 3, 6, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456605783 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783 Building ZINC001456605783 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456605783 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 824) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(c3ccco3)nn2c2cccc(C)c2)cc1Cl) `ZINC001456605783.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456605783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001456605783 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(c3ccco3)nn2c2cccc(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.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 16, 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, 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] 0 hydrogens 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, 1, 3, 3, 4, 7, 7, 7, 12, 12, 12, 12, 7, 7, 7, 13, 13, 13, 13, 13, 13, 6, 6, 6, 10, 10, 10, 6, 6, 4, 7, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 825) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3ccco3)nn2c2cccc(C)c2)cc1Cl) `ZINC001456605783.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456605783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001456605783 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3ccco3)nn2c2cccc(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.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 16, 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, 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] 0 hydrogens 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, 1, 2, 2, 3, 6, 6, 6, 11, 11, 11, 11, 6, 6, 6, 12, 12, 6, 12, 12, 12, 6, 6, 6, 10, 10, 10, 6, 6, 3, 6, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456605783 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456605783 Building ZINC001456621585 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456621585 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/826 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC001456621585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456621585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001456621585 none CCc1ccc(CCNC(=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', '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.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] 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: [12, 12, 12, 12, 12, 12, 8, 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, 8, 8, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 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, 52, 53, 54, 55]) total number of confs: 70 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/827 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/827' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC001456621585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456621585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001456621585 none CCc1ccc(CCNC(=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', '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.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] 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: [12, 12, 12, 12, 12, 12, 8, 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, 8, 8, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 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, 52, 53, 54, 55]) total number of confs: 74 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456621585 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585 Building ZINC001456621585 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456621585 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 826) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC001456621585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456621585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001456621585 none CCc1ccc(CCNC(=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', '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.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] 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: [12, 12, 12, 12, 12, 12, 8, 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, 8, 8, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 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, 52, 53, 54, 55]) total number of confs: 70 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 827) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC001456621585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456621585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001456621585 none CCc1ccc(CCNC(=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', '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.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] 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: [12, 12, 12, 12, 12, 12, 8, 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, 8, 8, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 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, 52, 53, 54, 55]) total number of confs: 74 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456621585 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456621585 Building ZINC001456639856 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456639856 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/828 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(n2nc(C(C)(C)C)cc2NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C)c1) `ZINC001456639856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456639856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001456639856 none Cc1ccc(n2nc(C(C)(C)C)cc2NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', '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.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, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 13, 13, 13, 13, 13, 19, 19, 19, 13, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21] 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, 59]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/829 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/829' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(n2nc(C(C)(C)C)cc2NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C)c1) `ZINC001456639856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456639856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001456639856 none Cc1ccc(n2nc(C(C)(C)C)cc2NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', '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.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, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 20, 20, 13, 13, 13, 13, 13, 19, 19, 19, 13, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20] 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, 59]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456639856 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856 Building ZINC001456639856 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456639856 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 828) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(n2nc(C(C)(C)C)cc2NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C)c1) `ZINC001456639856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456639856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001456639856 none Cc1ccc(n2nc(C(C)(C)C)cc2NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', '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.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, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 13, 13, 13, 13, 13, 19, 19, 19, 13, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21] 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, 59]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 829) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(n2nc(C(C)(C)C)cc2NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C)c1) `ZINC001456639856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456639856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001456639856 none Cc1ccc(n2nc(C(C)(C)C)cc2NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', '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.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, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 20, 20, 13, 13, 13, 13, 13, 19, 19, 19, 13, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20] 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, 59]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456639856 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456639856 Building ZINC001456695410 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456695410 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/830 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001456695410.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456695410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001456695410 none CCc1ccccc1CNC(=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.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.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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 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, 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] 0 hydrogens 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, 8, 12, 7, 12, 12, 7, 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, 8, 12, 12, 7, 7, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2] 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]) total number of confs: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/831 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/831' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001456695410.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456695410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001456695410 none CCc1ccccc1CNC(=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.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.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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 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, 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] 0 hydrogens 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, 8, 12, 10, 12, 12, 7, 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, 10, 12, 12, 7, 7, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456695410 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410 Building ZINC001456695410 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456695410 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 830) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001456695410.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456695410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001456695410 none CCc1ccccc1CNC(=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.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.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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 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, 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] 0 hydrogens 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, 8, 12, 7, 12, 12, 7, 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, 8, 12, 12, 7, 7, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2] 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]) total number of confs: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 831) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001456695410.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456695410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001456695410 none CCc1ccccc1CNC(=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.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.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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 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, 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] 0 hydrogens 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, 8, 12, 10, 12, 12, 7, 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, 10, 12, 12, 7, 7, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456695410 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456695410 Building ZINC001456876871 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456876871 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/832 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Oc1ccc(Br)cc1) `ZINC001456876871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456876871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001456876871 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Oc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 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, 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, 13, 24, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 46, 47, 47, 47, 47, 47, 47, 24, 24, 24, 13, 13, 2, 3, 1, 3, 47, 47, 47, 47] 50 rigid atoms, others: [5, 7, 8, 9] 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]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/833 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/833' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Oc1ccc(Br)cc1) `ZINC001456876871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456876871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001456876871 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Oc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 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, 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: [25, 12, 26, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 26, 46, 47, 47, 47, 47, 47, 47, 26, 26, 26, 12, 12, 2, 3, 1, 3, 47, 47, 47, 47] 50 rigid atoms, others: [5, 7, 8, 9] 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456876871 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871 Building ZINC001456876871 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456876871 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 832) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Oc1ccc(Br)cc1) `ZINC001456876871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456876871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001456876871 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Oc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 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, 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, 13, 24, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 46, 47, 47, 47, 47, 47, 47, 24, 24, 24, 13, 13, 2, 3, 1, 3, 47, 47, 47, 47] 50 rigid atoms, others: [5, 7, 8, 9] 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]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 833) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Oc1ccc(Br)cc1) `ZINC001456876871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456876871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001456876871 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Oc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 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, 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: [25, 12, 26, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 26, 46, 47, 47, 47, 47, 47, 47, 26, 26, 26, 12, 12, 2, 3, 1, 3, 47, 47, 47, 47] 50 rigid atoms, others: [5, 7, 8, 9] 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456876871 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876871 Building ZINC001456876875 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456876875 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/834 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Oc1ccc(Br)cc1) `ZINC001456876875.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456876875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001456876875 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Oc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 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, 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: [25, 12, 26, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 26, 46, 47, 47, 47, 47, 47, 47, 26, 26, 26, 12, 12, 2, 3, 1, 3, 47, 47, 47, 47] 50 rigid atoms, others: [5, 7, 8, 9] 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/835 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/835' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Oc1ccc(Br)cc1) `ZINC001456876875.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456876875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001456876875 none C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Oc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 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, 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, 13, 24, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 46, 47, 47, 46, 47, 47, 47, 24, 24, 24, 13, 13, 2, 3, 1, 3, 47, 47, 47, 47] 50 rigid atoms, others: [5, 7, 8, 9] 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456876875 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875 Building ZINC001456876875 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456876875 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 834) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Oc1ccc(Br)cc1) `ZINC001456876875.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456876875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001456876875 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Oc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 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, 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: [25, 12, 26, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 26, 46, 47, 47, 47, 47, 47, 47, 26, 26, 26, 12, 12, 2, 3, 1, 3, 47, 47, 47, 47] 50 rigid atoms, others: [5, 7, 8, 9] 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 835) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Oc1ccc(Br)cc1) `ZINC001456876875.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456876875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001456876875 none C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Oc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 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, 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, 13, 24, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 46, 47, 47, 46, 47, 47, 47, 24, 24, 24, 13, 13, 2, 3, 1, 3, 47, 47, 47, 47] 50 rigid atoms, others: [5, 7, 8, 9] 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456876875 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456876875 Building ZINC001456917923 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456917923 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/836 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(cc(F)cc2Br)s1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001456917923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456917923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001456917923 none O=C(Nc1nc2c(cc(F)cc2Br)s1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 15, 1, 1, 17, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 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: [11, 1, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 19, 19, 8, 8, 8, 8] 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]) total number of confs: 47 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/837 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/837' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(cc(F)cc2Br)s1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001456917923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456917923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001456917923 none O=C(Nc1nc2c(cc(F)cc2Br)s1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 15, 1, 1, 17, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 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: [11, 1, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 19, 19, 8, 8, 8, 8] 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]) total number of confs: 47 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456917923 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923 Building ZINC001456917923 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456917923 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 836) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1nc2c(cc(F)cc2Br)s1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001456917923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456917923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001456917923 none O=C(Nc1nc2c(cc(F)cc2Br)s1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 15, 1, 1, 17, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 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: [11, 1, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 19, 19, 8, 8, 8, 8] 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]) total number of confs: 47 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 837) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1nc2c(cc(F)cc2Br)s1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001456917923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456917923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001456917923 none O=C(Nc1nc2c(cc(F)cc2Br)s1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 15, 1, 1, 17, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 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: [11, 1, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 19, 19, 8, 8, 8, 8] 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]) total number of confs: 47 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456917923 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456917923 Building ZINC001456978735 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456978735 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/838 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(Br)c(C)c1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456978735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456978735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001456978735 none COC(=O)c1ccc(Br)c(C)c1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 17, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 42, 18, 43, 18, 18, 5, 18, 18, 18, 18, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 2, 4, 4, 4, 43, 43, 43, 18, 18, 18, 18, 18, 5, 4, 2, 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]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/839 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/839' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(Br)c(C)c1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456978735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456978735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001456978735 none COC(=O)c1ccc(Br)c(C)c1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 17, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 42, 18, 43, 18, 18, 10, 18, 18, 18, 18, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 43, 43, 43, 18, 18, 18, 18, 18, 5, 4, 1, 4] 50 rigid atoms, others: [13, 15, 16, 17] 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456978735 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735 Building ZINC001456978735 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456978735 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 838) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COC(=O)c1ccc(Br)c(C)c1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456978735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456978735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001456978735 none COC(=O)c1ccc(Br)c(C)c1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 17, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 42, 18, 43, 18, 18, 5, 18, 18, 18, 18, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 2, 4, 4, 4, 43, 43, 43, 18, 18, 18, 18, 18, 5, 4, 2, 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]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 839) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COC(=O)c1ccc(Br)c(C)c1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456978735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456978735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001456978735 none COC(=O)c1ccc(Br)c(C)c1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 17, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 42, 18, 43, 18, 18, 10, 18, 18, 18, 18, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 43, 43, 43, 18, 18, 18, 18, 18, 5, 4, 1, 4] 50 rigid atoms, others: [13, 15, 16, 17] 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001456978735 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001456978735 Building ZINC001457020529 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457020529 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/840 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccc(C(F)(F)F)cc3)cc2)cn1) `ZINC001457020529.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457020529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001457020529 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccc(C(F)(F)F)cc3)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 9, 9, 43, 45, 45, 43, 43, 45, 45, 45, 45, 45, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 15, 15, 45, 45, 45, 45, 15, 15, 4] 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]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/841 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/841' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccc(C(F)(F)F)cc3)cc2)cn1) `ZINC001457020529.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457020529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001457020529 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccc(C(F)(F)F)cc3)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 13, 16, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 16, 16, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 2, 10, 10, 16, 16, 45, 45, 45, 45, 16, 16, 4] 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457020529 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529 Building ZINC001457020529 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457020529 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 840) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccc(C(F)(F)F)cc3)cc2)cn1) `ZINC001457020529.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457020529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001457020529 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccc(C(F)(F)F)cc3)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 9, 9, 43, 45, 45, 43, 43, 45, 45, 45, 45, 45, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 15, 15, 45, 45, 45, 45, 15, 15, 4] 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]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 841) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccc(C(F)(F)F)cc3)cc2)cn1) `ZINC001457020529.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457020529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001457020529 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Oc3ccc(C(F)(F)F)cc3)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 13, 16, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 16, 16, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 2, 10, 10, 16, 16, 45, 45, 45, 45, 16, 16, 4] 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457020529 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457020529 Building ZINC001457088586 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457088586 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/842 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1cccc(c2ccncc2)c1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001457088586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457088586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457088586 none CCN(Cc1cccc(c2ccncc2)c1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 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: [7, 6, 3, 6, 11, 22, 22, 22, 22, 22, 27, 27, 22, 27, 27, 22, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 11, 11, 22, 22, 22, 27, 27, 27, 27, 22, 6, 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]) total number of confs: 95 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/843 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/843' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1cccc(c2ccncc2)c1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001457088586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457088586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457088586 none CCN(Cc1cccc(c2ccncc2)c1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 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: [6, 5, 3, 5, 9, 19, 19, 19, 19, 19, 25, 25, 19, 25, 25, 19, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 9, 9, 19, 19, 19, 25, 25, 25, 25, 19, 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]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457088586 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586 Building ZINC001457088586 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457088586 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 842) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/842: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Cc1cccc(c2ccncc2)c1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001457088586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457088586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457088586 none CCN(Cc1cccc(c2ccncc2)c1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 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: [7, 6, 3, 6, 11, 22, 22, 22, 22, 22, 27, 27, 22, 27, 27, 22, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 11, 11, 22, 22, 22, 27, 27, 27, 27, 22, 6, 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]) total number of confs: 95 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 843) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/843: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Cc1cccc(c2ccncc2)c1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001457088586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457088586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457088586 none CCN(Cc1cccc(c2ccncc2)c1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 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: [6, 5, 3, 5, 9, 19, 19, 19, 19, 19, 25, 25, 19, 25, 25, 19, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 9, 9, 19, 19, 19, 25, 25, 25, 25, 19, 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]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457088586 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457088586 Building ZINC001457263589 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457263589 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/844 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2Oc2ccc(Cl)cc2)cn1) `ZINC001457263589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457263589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001457263589 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2Oc2ccc(Cl)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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 17, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 5, 5, 5, 15, 17, 17, 17, 17, 17, 17, 6, 6, 10, 10, 10, 10, 10, 6, 2, 5, 5, 5, 17, 17, 17, 17, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/845 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/845' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2Oc2ccc(Cl)cc2)cn1) `ZINC001457263589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457263589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001457263589 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2Oc2ccc(Cl)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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 17, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 2, 4, 4, 4, 14, 15, 15, 14, 15, 15, 15, 6, 6, 10, 10, 10, 10, 10, 6, 2, 4, 4, 4, 15, 15, 15, 15, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457263589 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589 Building ZINC001457263589 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457263589 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 844) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2Oc2ccc(Cl)cc2)cn1) `ZINC001457263589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457263589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001457263589 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2Oc2ccc(Cl)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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 17, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 5, 5, 5, 15, 17, 17, 17, 17, 17, 17, 6, 6, 10, 10, 10, 10, 10, 6, 2, 5, 5, 5, 17, 17, 17, 17, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 845) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2Oc2ccc(Cl)cc2)cn1) `ZINC001457263589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457263589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001457263589 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2Oc2ccc(Cl)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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 17, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 2, 4, 4, 4, 14, 15, 15, 14, 15, 15, 15, 6, 6, 10, 10, 10, 10, 10, 6, 2, 4, 4, 4, 15, 15, 15, 15, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457263589 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457263589 Building ZINC001457400774 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457400774 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/846 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOCCN(C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)c1cccc(Br)c1) `ZINC001457400774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457400774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001457400774 none CCCCOCCN(C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)c1cccc(Br)c1 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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 17, 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, 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] 0 hydrogens 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, 8, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 19, 19, 8, 8, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/847 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/847' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOCCN(C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)c1cccc(Br)c1) `ZINC001457400774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457400774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001457400774 none CCCCOCCN(C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)c1cccc(Br)c1 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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 17, 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, 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] 0 hydrogens 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, 26, 16, 4, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 24, 26, 26, 26, 26, 26, 26, 16, 16, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [45, 43, 17, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 18, 19, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48, 49]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457400774 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774 Building ZINC001457400774 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457400774 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 846) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCCOCCN(C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)c1cccc(Br)c1) `ZINC001457400774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457400774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001457400774 none CCCCOCCN(C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)c1cccc(Br)c1 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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 17, 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, 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] 0 hydrogens 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, 8, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 19, 19, 8, 8, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 847) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCCCOCCN(C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)c1cccc(Br)c1) `ZINC001457400774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457400774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001457400774 none CCCCOCCN(C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)c1cccc(Br)c1 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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 1, 17, 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, 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] 0 hydrogens 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, 26, 16, 4, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 24, 26, 26, 26, 26, 26, 26, 16, 16, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [45, 43, 17, 8, 41, 10, 11, 12, 13, 14, 15, 16, 40, 18, 19, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48, 49]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457400774 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457400774 Building ZINC001457417491 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457417491 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/848 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2n[nH]c(C)c2c2ccc(Br)cc2)cc1Cl) `ZINC001457417491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457417491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457417491 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2n[nH]c(C)c2c2ccc(Br)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.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 1, 8, 8, 6, 1, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 22, 22, 13, 17, 22, 22, 6, 6, 6, 12, 12, 12, 6, 6, 4, 13, 13, 13, 22, 22, 22, 22, 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, 40, 41]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/849 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/849' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2n[nH]c(C)c2c2ccc(Br)cc2)cc1Cl) `ZINC001457417491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457417491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457417491 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2n[nH]c(C)c2c2ccc(Br)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.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 1, 8, 8, 6, 1, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 22, 22, 13, 20, 22, 22, 6, 6, 6, 12, 12, 12, 6, 6, 4, 13, 13, 13, 22, 22, 22, 22, 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, 40, 41]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457417491 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491 Building ZINC001457417491 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457417491 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 848) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2n[nH]c(C)c2c2ccc(Br)cc2)cc1Cl) `ZINC001457417491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457417491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457417491 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2n[nH]c(C)c2c2ccc(Br)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.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 1, 8, 8, 6, 1, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 22, 22, 13, 17, 22, 22, 6, 6, 6, 12, 12, 12, 6, 6, 4, 13, 13, 13, 22, 22, 22, 22, 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, 40, 41]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 849) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2n[nH]c(C)c2c2ccc(Br)cc2)cc1Cl) `ZINC001457417491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457417491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457417491 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2n[nH]c(C)c2c2ccc(Br)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.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 1, 8, 8, 6, 1, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 22, 22, 13, 20, 22, 22, 6, 6, 6, 12, 12, 12, 6, 6, 4, 13, 13, 13, 22, 22, 22, 22, 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, 40, 41]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457417491 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457417491 Building ZINC001457428114 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457428114 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/850 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/850' -> `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)N1CCc2ccc(Cl)cc21) `ZINC001457428114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457428114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457428114 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(Cl)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', '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, 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, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 19, 19, 3, 19, 3, 3, 3, 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]) total number of confs: 62 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/851 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/851' -> `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)N1CCc2ccc(Cl)cc21) `ZINC001457428114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457428114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457428114 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccc(Cl)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', '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, 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, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 5, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 2, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 18, 18, 14, 18, 3, 3, 3, 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]) total number of confs: 70 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457428114 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114 Building ZINC001457428114 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457428114 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 850) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(Cl)cc21) `ZINC001457428114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457428114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457428114 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(Cl)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', '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, 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, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 19, 19, 3, 19, 3, 3, 3, 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]) total number of confs: 62 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 851) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccc(Cl)cc21) `ZINC001457428114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457428114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457428114 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccc(Cl)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', '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, 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, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 5, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 2, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 18, 18, 14, 18, 3, 3, 3, 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]) total number of confs: 70 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457428114 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457428114 Building ZINC001457430102 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457430102 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/852 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ccccc1)C1Cc2ccccc2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001457430102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457430102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001457430102 none O=C(N(c1ccccc1)C1Cc2ccccc2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [5, 1, 5, 9, 15, 15, 12, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 30, 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]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/853 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/853' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ccccc1)C1Cc2ccccc2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001457430102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457430102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001457430102 none O=C(N(c1ccccc1)C1Cc2ccccc2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [5, 1, 5, 9, 15, 15, 9, 15, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 12, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 31, 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]) total number of confs: 119 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457430102 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102 Building ZINC001457430102 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457430102 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 852) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N(c1ccccc1)C1Cc2ccccc2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001457430102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457430102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001457430102 none O=C(N(c1ccccc1)C1Cc2ccccc2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [5, 1, 5, 9, 15, 15, 12, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 30, 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]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 853) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N(c1ccccc1)C1Cc2ccccc2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001457430102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457430102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001457430102 none O=C(N(c1ccccc1)C1Cc2ccccc2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [5, 1, 5, 9, 15, 15, 9, 15, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 12, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 31, 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]) total number of confs: 119 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457430102 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457430102 Building ZINC001457440554 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457440554 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/854 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncccc2OCc2cccc(Cl)c2)cc1Cl) `ZINC001457440554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457440554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001457440554 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncccc2OCc2cccc(Cl)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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 4, 4, 4, 4, 10, 15, 29, 29, 29, 29, 29, 29, 3, 3, 3, 5, 5, 5, 3, 3, 2, 4, 4, 4, 15, 15, 29, 29, 29, 29, 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/855 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/855' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncccc2OCc2cccc(Cl)c2)cc1Cl) `ZINC001457440554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457440554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001457440554 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncccc2OCc2cccc(Cl)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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 4, 4, 4, 4, 10, 16, 30, 30, 30, 30, 30, 30, 3, 3, 3, 5, 5, 5, 3, 3, 2, 4, 4, 4, 16, 16, 30, 30, 30, 30, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457440554 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554 Building ZINC001457440554 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457440554 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 854) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncccc2OCc2cccc(Cl)c2)cc1Cl) `ZINC001457440554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457440554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001457440554 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncccc2OCc2cccc(Cl)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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 4, 4, 4, 4, 10, 15, 29, 29, 29, 29, 29, 29, 3, 3, 3, 5, 5, 5, 3, 3, 2, 4, 4, 4, 15, 15, 29, 29, 29, 29, 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 855) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncccc2OCc2cccc(Cl)c2)cc1Cl) `ZINC001457440554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457440554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001457440554 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncccc2OCc2cccc(Cl)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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 4, 4, 4, 4, 10, 16, 30, 30, 30, 30, 30, 30, 3, 3, 3, 5, 5, 5, 3, 3, 2, 4, 4, 4, 16, 16, 30, 30, 30, 30, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457440554 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457440554 Building ZINC001457457071 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457457071 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/856 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](c1ccc(Cl)cc1)c1cnccn1) `ZINC001457457071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457457071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001457457071 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](c1ccc(Cl)cc1)c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 11, 29, 29, 37, 37, 29, 29, 37, 37, 29, 50, 50, 50, 50, 50, 11, 11, 11, 2, 1, 2, 37, 37, 37, 37, 50, 50, 50] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/857 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/857' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](c1ccc(Cl)cc1)c1cnccn1) `ZINC001457457071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457457071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001457457071 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](c1ccc(Cl)cc1)c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 10, 25, 25, 31, 31, 25, 25, 31, 31, 25, 48, 48, 48, 48, 48, 10, 10, 10, 2, 1, 2, 31, 31, 31, 31, 48, 48, 48] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457457071 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071 Building ZINC001457457071 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457457071 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 856) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](c1ccc(Cl)cc1)c1cnccn1) `ZINC001457457071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457457071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001457457071 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](c1ccc(Cl)cc1)c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 11, 29, 29, 37, 37, 29, 29, 37, 37, 29, 50, 50, 50, 50, 50, 11, 11, 11, 2, 1, 2, 37, 37, 37, 37, 50, 50, 50] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 857) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](c1ccc(Cl)cc1)c1cnccn1) `ZINC001457457071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457457071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001457457071 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](c1ccc(Cl)cc1)c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 10, 25, 25, 31, 31, 25, 25, 31, 31, 25, 48, 48, 48, 48, 48, 10, 10, 10, 2, 1, 2, 31, 31, 31, 31, 48, 48, 48] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457457071 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457071 Building ZINC001457457191 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457457191 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/858 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](c1ccc(Cl)cc1)c1cnccn1) `ZINC001457457191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457457191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001457457191 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](c1ccc(Cl)cc1)c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 10, 26, 26, 31, 31, 26, 26, 31, 31, 26, 48, 48, 48, 48, 48, 10, 10, 10, 2, 1, 2, 31, 31, 31, 31, 48, 48, 48] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/859 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/859' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](c1ccc(Cl)cc1)c1cnccn1) `ZINC001457457191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457457191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001457457191 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](c1ccc(Cl)cc1)c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 11, 30, 30, 37, 37, 30, 30, 37, 37, 30, 50, 50, 50, 50, 50, 11, 11, 11, 2, 1, 2, 37, 37, 37, 37, 50, 50, 50] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457457191 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191 Building ZINC001457457191 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457457191 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 858) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](c1ccc(Cl)cc1)c1cnccn1) `ZINC001457457191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457457191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001457457191 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](c1ccc(Cl)cc1)c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 10, 26, 26, 31, 31, 26, 26, 31, 31, 26, 48, 48, 48, 48, 48, 10, 10, 10, 2, 1, 2, 31, 31, 31, 31, 48, 48, 48] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 859) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](c1ccc(Cl)cc1)c1cnccn1) `ZINC001457457191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457457191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001457457191 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](c1ccc(Cl)cc1)c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 11, 30, 30, 37, 37, 30, 30, 37, 37, 30, 50, 50, 50, 50, 50, 11, 11, 11, 2, 1, 2, 37, 37, 37, 37, 50, 50, 50] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457457191 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457457191 Building ZINC001457458513 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457458513 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/860 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1cc(F)ccc1F)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001457458513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457458513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001457458513 none O=C(c1cc(F)ccc1F)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 15, 1, 1, 1, 15, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 29, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 3, 2, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 5, 5, 5, 5, 5, 1, 1, 1, 5, 5, 5, 5] 50 rigid atoms, others: [36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/861 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/861' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1cc(F)ccc1F)C1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001457458513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457458513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001457458513 none O=C(c1cc(F)ccc1F)C1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 15, 1, 1, 1, 15, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 6, 34, 49, 49, 49, 49, 49, 49, 49, 6, 6, 6, 4, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 6, 6, 49, 49, 49, 6, 6, 6, 6, 6, 3, 3, 3, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457458513 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513 Building ZINC001457458513 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457458513 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 860) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c1cc(F)ccc1F)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001457458513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457458513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001457458513 none O=C(c1cc(F)ccc1F)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 15, 1, 1, 1, 15, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 29, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 3, 2, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 5, 5, 5, 5, 5, 1, 1, 1, 5, 5, 5, 5] 50 rigid atoms, others: [36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 861) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c1cc(F)ccc1F)C1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001457458513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457458513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001457458513 none O=C(c1cc(F)ccc1F)C1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 15, 1, 1, 1, 15, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 6, 34, 49, 49, 49, 49, 49, 49, 49, 6, 6, 6, 4, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 6, 6, 49, 49, 49, 6, 6, 6, 6, 6, 3, 3, 3, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457458513 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457458513 Building ZINC001457472298 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457472298 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/862 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2cc(F)ccc2OC)c1) `ZINC001457472298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457472298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001457472298 none COc1cccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2cc(F)ccc2OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 27, 27, 27, 27, 27, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 8, 17, 17, 17, 10, 17, 17, 17, 22, 27, 34, 34, 34, 27, 27, 27, 4, 3, 3, 3, 3, 17, 8, 17, 22, 22, 22, 27] 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]) total number of confs: 125 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/863 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/863' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2cc(F)ccc2OC)c1) `ZINC001457472298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457472298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001457472298 none COc1cccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2cc(F)ccc2OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 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, 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] 0 hydrogens 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, 28, 28, 28, 28, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 15, 15, 15, 10, 15, 15, 15, 19, 28, 37, 37, 37, 28, 28, 28, 4, 3, 3, 3, 3, 15, 8, 15, 19, 19, 19, 28] 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]) total number of confs: 117 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457472298 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298 Building ZINC001457472298 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457472298 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 862) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1cccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2cc(F)ccc2OC)c1) `ZINC001457472298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457472298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001457472298 none COc1cccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2cc(F)ccc2OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 27, 27, 27, 27, 27, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 8, 17, 17, 17, 10, 17, 17, 17, 22, 27, 34, 34, 34, 27, 27, 27, 4, 3, 3, 3, 3, 17, 8, 17, 22, 22, 22, 27] 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]) total number of confs: 125 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 863) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1cccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2cc(F)ccc2OC)c1) `ZINC001457472298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457472298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001457472298 none COc1cccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2cc(F)ccc2OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 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, 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] 0 hydrogens 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, 28, 28, 28, 28, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 15, 15, 15, 10, 15, 15, 15, 19, 28, 37, 37, 37, 28, 28, 28, 4, 3, 3, 3, 3, 15, 8, 15, 19, 19, 19, 28] 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]) total number of confs: 117 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457472298 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472298 Building ZINC001457472302 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457472302 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/864 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2cc(F)ccc2OC)c1) `ZINC001457472302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457472302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001457472302 none COc1cccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2cc(F)ccc2OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 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, 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] 0 hydrogens 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, 28, 28, 28, 28, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 15, 15, 15, 13, 15, 15, 15, 19, 28, 37, 37, 37, 28, 28, 28, 4, 3, 3, 3, 3, 15, 10, 15, 19, 19, 19, 28] 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]) total number of confs: 111 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/865 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/865' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2cc(F)ccc2OC)c1) `ZINC001457472302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457472302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001457472302 none COc1cccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2cc(F)ccc2OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 27, 27, 27, 27, 27, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 17, 17, 17, 17, 17, 17, 17, 22, 27, 34, 34, 34, 27, 27, 27, 4, 3, 3, 3, 3, 17, 17, 17, 22, 22, 22, 27] 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]) total number of confs: 103 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457472302 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302 Building ZINC001457472302 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457472302 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 864) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1cccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2cc(F)ccc2OC)c1) `ZINC001457472302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457472302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001457472302 none COc1cccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2cc(F)ccc2OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 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, 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] 0 hydrogens 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, 28, 28, 28, 28, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 15, 15, 15, 13, 15, 15, 15, 19, 28, 37, 37, 37, 28, 28, 28, 4, 3, 3, 3, 3, 15, 10, 15, 19, 19, 19, 28] 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]) total number of confs: 111 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 865) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1cccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2cc(F)ccc2OC)c1) `ZINC001457472302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457472302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001457472302 none COc1cccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2cc(F)ccc2OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 27, 27, 27, 27, 27, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 17, 17, 17, 17, 17, 17, 17, 22, 27, 34, 34, 34, 27, 27, 27, 4, 3, 3, 3, 3, 17, 17, 17, 22, 22, 22, 27] 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]) total number of confs: 103 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457472302 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457472302 Building ZINC001457495132 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457495132 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/866 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c(c2nc(C3CC3)no2)c1) `ZINC001457495132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457495132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001457495132 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c(c2nc(C3CC3)no2)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', 'Br', 'S.3', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.ar', '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, 17, 14, 1, 1, 8, 1, 5, 5, 5, 8, 12, 1, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 30, 30, 30, 46, 46, 30, 30, 7, 7, 7, 7, 7, 7, 3, 4, 4, 46, 46, 46, 46, 46, 7] 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/867 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/867' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c(c2nc(C3CC3)no2)c1) `ZINC001457495132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457495132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001457495132 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c(c2nc(C3CC3)no2)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', 'Br', 'S.3', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.ar', '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, 17, 14, 1, 1, 8, 1, 5, 5, 5, 8, 12, 1, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 30, 30, 30, 46, 46, 30, 30, 7, 7, 7, 7, 7, 7, 3, 4, 4, 46, 46, 46, 46, 46, 7] 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457495132 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132 Building ZINC001457495132 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457495132 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 866) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c(c2nc(C3CC3)no2)c1) `ZINC001457495132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457495132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001457495132 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c(c2nc(C3CC3)no2)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', 'Br', 'S.3', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.ar', '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, 17, 14, 1, 1, 8, 1, 5, 5, 5, 8, 12, 1, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 30, 30, 30, 46, 46, 30, 30, 7, 7, 7, 7, 7, 7, 3, 4, 4, 46, 46, 46, 46, 46, 7] 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 867) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c(c2nc(C3CC3)no2)c1) `ZINC001457495132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457495132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001457495132 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c(c2nc(C3CC3)no2)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', 'Br', 'S.3', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.ar', '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, 17, 14, 1, 1, 8, 1, 5, 5, 5, 8, 12, 1, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 30, 30, 30, 46, 46, 30, 30, 7, 7, 7, 7, 7, 7, 3, 4, 4, 46, 46, 46, 46, 46, 7] 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457495132 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457495132 Building ZINC001457519520 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457519520 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/868 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1c1ccc(CN2CCCC2)cc1) `ZINC001457519520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457519520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001457519520 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1c1ccc(CN2CCCC2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', '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', '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, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 1, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 49, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2, 2, 2, 3, 17, 17, 24, 24, 24, 24, 24, 24, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/869 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/869' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1ccccc1c1ccc(CN2CCCC2)cc1) `ZINC001457519520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457519520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001457519520 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1ccccc1c1ccc(CN2CCCC2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', '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', '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, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 1, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 18, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 49, 50, 50, 50, 50, 25, 25, 2, 2, 2, 2, 2, 2, 3, 18, 18, 25, 25, 25, 25, 25, 25, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25] 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]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457519520 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520 Building ZINC001457519520 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457519520 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 868) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1c1ccc(CN2CCCC2)cc1) `ZINC001457519520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457519520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001457519520 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1c1ccc(CN2CCCC2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', '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', '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, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 1, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 49, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2, 2, 2, 3, 17, 17, 24, 24, 24, 24, 24, 24, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 869) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1ccccc1c1ccc(CN2CCCC2)cc1) `ZINC001457519520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457519520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001457519520 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1ccccc1c1ccc(CN2CCCC2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', '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', '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, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 1, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 18, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 49, 50, 50, 50, 50, 25, 25, 2, 2, 2, 2, 2, 2, 3, 18, 18, 25, 25, 25, 25, 25, 25, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25] 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]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457519520 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457519520 Building ZINC001457552325 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457552325 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/870 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(SCc2cccs2)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001457552325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457552325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001457552325 none O=C(Nc1nnc(SCc2cccs2)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 14, 5, 1, 1, 1, 1, 14, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 22, 35, 47, 47, 47, 47, 4, 1, 1, 1, 4, 4, 4, 4, 4, 2, 35, 35, 47, 47, 47, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/871 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/871' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(SCc2cccs2)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001457552325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457552325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001457552325 none O=C(Nc1nnc(SCc2cccs2)s1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 14, 5, 1, 1, 1, 1, 14, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 22, 35, 47, 47, 47, 47, 4, 1, 1, 1, 4, 4, 4, 4, 4, 2, 35, 35, 47, 47, 47, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457552325 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325 Building ZINC001457552325 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457552325 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 870) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1nnc(SCc2cccs2)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001457552325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457552325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001457552325 none O=C(Nc1nnc(SCc2cccs2)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 14, 5, 1, 1, 1, 1, 14, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 22, 35, 47, 47, 47, 47, 4, 1, 1, 1, 4, 4, 4, 4, 4, 2, 35, 35, 47, 47, 47, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 871) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1nnc(SCc2cccs2)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001457552325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457552325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001457552325 none O=C(Nc1nnc(SCc2cccs2)s1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 14, 5, 1, 1, 1, 1, 14, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 22, 35, 47, 47, 47, 47, 4, 1, 1, 1, 4, 4, 4, 4, 4, 2, 35, 35, 47, 47, 47, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457552325 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457552325 Building ZINC001457576992 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457576992 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/872 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/872' -> `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)NCc1ccc(C)cc1OCCC(C)C) `ZINC001457576992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457576992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001457576992 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(C)cc1OCCC(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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 12, 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] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 14, 14, 14, 14, 14, 14, 14, 21, 39, 49, 49, 49, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 9, 9, 14, 14, 14, 14, 14, 14, 39, 39, 49, 49, 49, 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, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/873 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/873' -> `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)NCc1ccc(C)cc1OCCC(C)C) `ZINC001457576992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457576992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001457576992 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(C)cc1OCCC(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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 12, 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] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 14, 14, 14, 14, 14, 14, 14, 22, 38, 48, 48, 48, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 8, 8, 14, 14, 14, 14, 14, 14, 38, 38, 48, 48, 48, 48, 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, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457576992 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992 Building ZINC001457576992 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457576992 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 872) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(C)cc1OCCC(C)C) `ZINC001457576992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457576992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001457576992 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(C)cc1OCCC(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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 12, 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] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 14, 14, 14, 14, 14, 14, 14, 21, 39, 49, 49, 49, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 9, 9, 14, 14, 14, 14, 14, 14, 39, 39, 49, 49, 49, 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, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 873) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(C)cc1OCCC(C)C) `ZINC001457576992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457576992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001457576992 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(C)cc1OCCC(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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 12, 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] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 14, 14, 14, 14, 14, 14, 14, 22, 38, 48, 48, 48, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 8, 8, 14, 14, 14, 14, 14, 14, 38, 38, 48, 48, 48, 48, 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, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457576992 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457576992 Building ZINC001457632892 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457632892 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/874 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/874' -> `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](c1ccccc1)c1cccc(F)c1) `ZINC001457632892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457632892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001457632892 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)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.ar', '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', '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', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 5, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 10, 10, 5, 10, 10, 5, 25, 25, 25, 25, 25, 25, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 3, 10, 10, 5, 10, 10, 25, 25, 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]) total number of confs: 79 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/875 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/875' -> `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](c1ccccc1)c1cccc(F)c1) `ZINC001457632892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457632892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001457632892 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)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.ar', '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', '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', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 10, 10, 6, 10, 10, 6, 28, 28, 28, 28, 28, 28, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 10, 10, 6, 10, 10, 28, 28, 28, 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, 51, 52, 53]) total number of confs: 80 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457632892 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892 Building ZINC001457632892 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457632892 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 874) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1cccc(F)c1) `ZINC001457632892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457632892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001457632892 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)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.ar', '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', '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', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 5, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 10, 10, 5, 10, 10, 5, 25, 25, 25, 25, 25, 25, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 3, 10, 10, 5, 10, 10, 25, 25, 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]) total number of confs: 79 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 875) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1cccc(F)c1) `ZINC001457632892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457632892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001457632892 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)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.ar', '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', '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', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 10, 10, 6, 10, 10, 6, 28, 28, 28, 28, 28, 28, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 10, 10, 6, 10, 10, 28, 28, 28, 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, 51, 52, 53]) total number of confs: 80 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457632892 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632892 Building ZINC001457632898 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457632898 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/876 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/876' -> `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](c1ccccc1)c1cccc(F)c1) `ZINC001457632898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457632898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001457632898 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)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.ar', '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', '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', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 10, 10, 6, 10, 10, 6, 27, 27, 27, 27, 27, 27, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 10, 10, 6, 10, 10, 27, 27, 27, 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: 86 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/877 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/877' -> `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](c1ccccc1)c1cccc(F)c1) `ZINC001457632898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457632898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001457632898 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)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.ar', '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', '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', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 10, 10, 6, 10, 10, 5, 26, 26, 26, 26, 26, 26, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 10, 10, 6, 10, 10, 26, 26, 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]) total number of confs: 78 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457632898 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898 Building ZINC001457632898 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457632898 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 876) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1cccc(F)c1) `ZINC001457632898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457632898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001457632898 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)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.ar', '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', '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', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 10, 10, 6, 10, 10, 6, 27, 27, 27, 27, 27, 27, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 10, 10, 6, 10, 10, 27, 27, 27, 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: 86 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 877) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1cccc(F)c1) `ZINC001457632898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457632898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001457632898 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)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.ar', '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', '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', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 10, 10, 6, 10, 10, 5, 26, 26, 26, 26, 26, 26, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 10, 10, 6, 10, 10, 26, 26, 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]) total number of confs: 78 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457632898 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457632898 Building ZINC001457662707 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457662707 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/878 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/878' -> `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)Nc1ccn(CCC(C)C)n1) `ZINC001457662707.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457662707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457662707 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccn(CCC(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.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom 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, 8, 5, 5, 5, 5, 5, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 4, 8, 10, 10, 10, 4, 3, 3, 3, 11, 11, 3, 11, 3, 3, 3, 2, 4, 4, 8, 8, 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, 55]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/879 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/879' -> `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)Nc1ccn(CCC(C)C)n1) `ZINC001457662707.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457662707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457662707 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccn(CCC(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.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom 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, 8, 5, 5, 5, 5, 5, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 4, 9, 10, 10, 10, 4, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 4, 4, 9, 9, 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, 55]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457662707 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707 Building ZINC001457662707 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457662707 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 878) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccn(CCC(C)C)n1) `ZINC001457662707.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457662707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457662707 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccn(CCC(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.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom 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, 8, 5, 5, 5, 5, 5, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 4, 8, 10, 10, 10, 4, 3, 3, 3, 11, 11, 3, 11, 3, 3, 3, 2, 4, 4, 8, 8, 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, 55]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 879) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccn(CCC(C)C)n1) `ZINC001457662707.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457662707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457662707 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccn(CCC(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.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom 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, 8, 5, 5, 5, 5, 5, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 4, 9, 10, 10, 10, 4, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 4, 4, 9, 9, 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, 55]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457662707 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457662707 Building ZINC001457743993 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457743993 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/880 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/880' -> `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(C)(C)C)CC1) `ZINC001457743993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457743993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457743993 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C(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', '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'] dock atom type 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, 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] dock 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: [4, 4, 4, 4, 4, 28, 28, 4, 28, 28, 28, 28, 28, 28, 4, 4, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 9, 9, 9, 7, 7, 4, 4, 4, 28, 28, 4, 28, 4, 4, 4, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 90 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/881 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/881' -> `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(C)(C)C)CC1) `ZINC001457743993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457743993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457743993 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C(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', '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'] dock atom type 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, 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] dock 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, 23, 23, 3, 23, 23, 23, 23, 23, 23, 3, 3, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 9, 9, 9, 7, 7, 3, 3, 3, 23, 23, 4, 23, 3, 3, 3, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 80 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457743993 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993 Building ZINC001457743993 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457743993 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 880) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C(C)(C)C)CC1) `ZINC001457743993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457743993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457743993 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C(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', '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'] dock atom type 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, 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] dock 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: [4, 4, 4, 4, 4, 28, 28, 4, 28, 28, 28, 28, 28, 28, 4, 4, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 9, 9, 9, 7, 7, 4, 4, 4, 28, 28, 4, 28, 4, 4, 4, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 90 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 881) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C(C)(C)C)CC1) `ZINC001457743993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457743993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457743993 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C(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', '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'] dock atom type 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, 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] dock 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, 23, 23, 3, 23, 23, 23, 23, 23, 23, 3, 3, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 9, 9, 9, 7, 7, 3, 3, 3, 23, 23, 4, 23, 3, 3, 3, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 80 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457743993 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457743993 Building ZINC001457749596 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457749596 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/882 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2cccc(F)c2)c2cccc(Br)c2)c1) `ZINC001457749596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457749596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457749596 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2cccc(F)c2)c2cccc(Br)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', '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', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 5, 5, 14, 14, 14, 14, 14, 14, 5, 15, 15, 13, 15, 15, 15, 4, 4, 4, 4, 2, 4, 4, 3, 14, 14, 14, 14, 15, 15, 14, 15, 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: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/883 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/883' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@H](c2cccc(F)c2)c2cccc(Br)c2)c1) `ZINC001457749596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457749596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457749596 none Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@H](c2cccc(F)c2)c2cccc(Br)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', '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', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 6, 6, 16, 16, 16, 16, 16, 16, 6, 15, 15, 12, 15, 15, 15, 4, 4, 4, 4, 2, 4, 4, 3, 16, 16, 16, 16, 15, 15, 15, 15, 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: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457749596 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596 Building ZINC001457749596 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457749596 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 882) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2cccc(F)c2)c2cccc(Br)c2)c1) `ZINC001457749596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457749596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457749596 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2cccc(F)c2)c2cccc(Br)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', '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', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 5, 5, 14, 14, 14, 14, 14, 14, 5, 15, 15, 13, 15, 15, 15, 4, 4, 4, 4, 2, 4, 4, 3, 14, 14, 14, 14, 15, 15, 14, 15, 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: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 883) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@H](c2cccc(F)c2)c2cccc(Br)c2)c1) `ZINC001457749596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457749596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457749596 none Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@H](c2cccc(F)c2)c2cccc(Br)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', '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', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 6, 6, 16, 16, 16, 16, 16, 16, 6, 15, 15, 12, 15, 15, 15, 4, 4, 4, 4, 2, 4, 4, 3, 16, 16, 16, 16, 15, 15, 15, 15, 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: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457749596 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749596 Building ZINC001457749597 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457749597 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/884 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(F)c2)c2cccc(Br)c2)c1) `ZINC001457749597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457749597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457749597 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(F)c2)c2cccc(Br)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', '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', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 6, 6, 15, 15, 15, 15, 15, 15, 6, 14, 14, 12, 14, 14, 14, 4, 4, 4, 4, 2, 4, 4, 3, 15, 15, 15, 15, 14, 14, 14, 14, 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: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/885 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/885' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(F)c2)c2cccc(Br)c2)c1) `ZINC001457749597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457749597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457749597 none Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(F)c2)c2cccc(Br)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', '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', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 5, 5, 14, 14, 14, 14, 14, 14, 5, 15, 15, 13, 15, 15, 15, 4, 4, 4, 4, 2, 4, 4, 3, 14, 14, 14, 14, 15, 15, 15, 15, 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457749597 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597 Building ZINC001457749597 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457749597 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 884) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(F)c2)c2cccc(Br)c2)c1) `ZINC001457749597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457749597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457749597 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(F)c2)c2cccc(Br)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', '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', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 6, 6, 15, 15, 15, 15, 15, 15, 6, 14, 14, 12, 14, 14, 14, 4, 4, 4, 4, 2, 4, 4, 3, 15, 15, 15, 15, 14, 14, 14, 14, 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: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 885) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(F)c2)c2cccc(Br)c2)c1) `ZINC001457749597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457749597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457749597 none Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(F)c2)c2cccc(Br)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', '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', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 1, 1, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 5, 5, 14, 14, 14, 14, 14, 14, 5, 15, 15, 13, 15, 15, 15, 4, 4, 4, 4, 2, 4, 4, 3, 14, 14, 14, 14, 15, 15, 15, 15, 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457749597 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457749597 Building ZINC001457891166 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457891166 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/886 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/886' -> `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(CCc1ccc(F)cc1)C1CCCC1) `ZINC001457891166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457891166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457891166 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCc1ccc(F)cc1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', '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'] 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, 15, 1, 1, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 7, 15, 16, 21, 21, 17, 21, 21, 21, 8, 16, 16, 16, 16, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 15, 15, 16, 16, 21, 21, 21, 21, 16, 16, 16, 16, 16, 16, 16, 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, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 138 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/887 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/887' -> `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(CCc1ccc(F)cc1)C1CCCC1) `ZINC001457891166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457891166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457891166 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCc1ccc(F)cc1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', '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'] 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, 15, 1, 1, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 6, 9, 9, 3, 3, 1, 1, 1, 1, 4, 4, 6, 18, 19, 25, 25, 19, 25, 25, 25, 7, 12, 12, 12, 12, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 18, 18, 19, 19, 25, 25, 25, 25, 12, 12, 12, 12, 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]) total number of confs: 155 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457891166 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166 Building ZINC001457891166 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457891166 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 886) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCc1ccc(F)cc1)C1CCCC1) `ZINC001457891166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457891166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457891166 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCc1ccc(F)cc1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', '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'] 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, 15, 1, 1, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 7, 15, 16, 21, 21, 17, 21, 21, 21, 8, 16, 16, 16, 16, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 15, 15, 16, 16, 21, 21, 21, 21, 16, 16, 16, 16, 16, 16, 16, 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, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 138 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 887) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCc1ccc(F)cc1)C1CCCC1) `ZINC001457891166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457891166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457891166 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCc1ccc(F)cc1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', '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'] 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, 15, 1, 1, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 6, 9, 9, 3, 3, 1, 1, 1, 1, 4, 4, 6, 18, 19, 25, 25, 19, 25, 25, 25, 7, 12, 12, 12, 12, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 18, 18, 19, 19, 25, 25, 25, 25, 12, 12, 12, 12, 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]) total number of confs: 155 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457891166 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457891166 Building ZINC001457933879 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457933879 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/888 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/888' -> `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](C2CCC2)C1) `ZINC001457933879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457933879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457933879 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.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, 5, 5, 7, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 4, 6, 6, 6, 6, 6, 6, 7, 15, 15, 15, 6, 2, 2, 2, 15, 15, 2, 15, 2, 2, 2, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 73 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/889 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/889' -> `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](C2CCC2)C1) `ZINC001457933879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457933879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457933879 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.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, 5, 5, 7, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 2, 3, 4, 5, 5, 5, 5, 5, 9, 16, 16, 16, 5, 2, 2, 2, 17, 17, 2, 17, 2, 2, 2, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 16, 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, 54, 55, 56]) total number of confs: 76 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457933879 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879 Building ZINC001457933879 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457933879 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 888) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C2CCC2)C1) `ZINC001457933879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457933879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457933879 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.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, 5, 5, 7, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 4, 6, 6, 6, 6, 6, 6, 7, 15, 15, 15, 6, 2, 2, 2, 15, 15, 2, 15, 2, 2, 2, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 73 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 889) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C2CCC2)C1) `ZINC001457933879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457933879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457933879 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.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, 5, 5, 7, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 2, 3, 4, 5, 5, 5, 5, 5, 9, 16, 16, 16, 5, 2, 2, 2, 17, 17, 2, 17, 2, 2, 2, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 16, 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, 54, 55, 56]) total number of confs: 76 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457933879 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933879 Building ZINC001457933882 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457933882 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/890 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/890' -> `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](C2CCC2)C1) `ZINC001457933882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457933882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457933882 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.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, 5, 5, 7, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 5, 17, 17, 17, 17, 17, 17, 2, 2, 1, 1, 1, 2, 3, 5, 6, 6, 6, 6, 6, 9, 15, 15, 15, 6, 2, 2, 2, 17, 17, 7, 17, 2, 2, 2, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 81 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/891 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/891' -> `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](C2CCC2)C1) `ZINC001457933882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457933882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457933882 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.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, 5, 5, 7, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 14, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 2, 4, 7, 7, 7, 7, 7, 7, 8, 12, 12, 12, 7, 2, 2, 2, 14, 14, 14, 14, 2, 2, 2, 7, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12, 7, 7] 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]) total number of confs: 46 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457933882 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882 Building ZINC001457933882 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457933882 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 890) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C2CCC2)C1) `ZINC001457933882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457933882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457933882 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.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, 5, 5, 7, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 5, 17, 17, 17, 17, 17, 17, 2, 2, 1, 1, 1, 2, 3, 5, 6, 6, 6, 6, 6, 9, 15, 15, 15, 6, 2, 2, 2, 17, 17, 7, 17, 2, 2, 2, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 81 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 891) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C2CCC2)C1) `ZINC001457933882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457933882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457933882 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.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, 5, 5, 7, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 14, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 2, 4, 7, 7, 7, 7, 7, 7, 8, 12, 12, 12, 7, 2, 2, 2, 14, 14, 14, 14, 2, 2, 2, 7, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12, 7, 7] 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]) total number of confs: 46 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457933882 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457933882 Building ZINC001457950144 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457950144 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/892 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc12) `ZINC001457950144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457950144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001457950144 none COC(=O)COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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] 0 hydrogens 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, 34, 50, 14, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 50, 50, 50, 34, 34, 6, 6, 2, 2, 1, 2, 6, 6, 6, 6] 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]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/893 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/893' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc12) `ZINC001457950144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457950144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001457950144 none COC(=O)COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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] 0 hydrogens 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, 35, 50, 16, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 50, 50, 50, 35, 35, 6, 6, 2, 2, 1, 2, 6, 6, 6, 6] 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]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457950144 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144 Building ZINC001457950144 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457950144 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 892) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc12) `ZINC001457950144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457950144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001457950144 none COC(=O)COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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] 0 hydrogens 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, 34, 50, 14, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 50, 50, 50, 34, 34, 6, 6, 2, 2, 1, 2, 6, 6, 6, 6] 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]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 893) grep: /scratch/xiaobo/182395/xbh-8058088.34/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)COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc12) `ZINC001457950144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457950144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001457950144 none COC(=O)COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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] 0 hydrogens 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, 35, 50, 16, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 50, 50, 50, 35, 35, 6, 6, 2, 2, 1, 2, 6, 6, 6, 6] 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]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457950144 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457950144 Building ZINC001457970680 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457970680 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/894 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/894' -> `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(Cl)cc(Cl)cc2C1) `ZINC001457970680.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457970680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001457970680 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2c(Cl)cc(Cl)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 16, 1, 1, 16, 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, 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] 0 hydrogens 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, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 2, 6, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19] 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]) total number of confs: 65 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/895 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/895' -> `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(Cl)cc(Cl)cc2C1) `ZINC001457970680.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457970680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001457970680 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2c(Cl)cc(Cl)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 16, 1, 1, 16, 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, 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] 0 hydrogens 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, 5, 14, 14, 4, 4, 1, 1, 1, 2, 6, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 14, 14, 7, 14, 14, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19] 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]) total number of confs: 71 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457970680 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680 Building ZINC001457970680 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457970680 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 894) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2c(Cl)cc(Cl)cc2C1) `ZINC001457970680.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457970680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001457970680 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2c(Cl)cc(Cl)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 16, 1, 1, 16, 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, 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] 0 hydrogens 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, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 2, 6, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19] 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]) total number of confs: 65 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 895) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2c(Cl)cc(Cl)cc2C1) `ZINC001457970680.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457970680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001457970680 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2c(Cl)cc(Cl)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 16, 1, 1, 16, 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, 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] 0 hydrogens 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, 5, 14, 14, 4, 4, 1, 1, 1, 2, 6, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 14, 14, 7, 14, 14, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19] 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]) total number of confs: 71 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457970680 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457970680 Building ZINC001457982872 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457982872 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/896 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/896' -> `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]2CCC[C@@H](C)C2)C1) `ZINC001457982872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457982872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457982872 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC([C@H]2CCC[C@@H](C)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.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', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 1, 2, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 3, 3, 17, 17, 17, 17, 3, 3, 3, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4] 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, 59]) total number of confs: 64 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/897 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/897' -> `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]2CCC[C@@H](C)C2)C1) `ZINC001457982872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457982872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457982872 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC([C@H]2CCC[C@@H](C)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.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', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 1, 2, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 5, 3, 3, 3, 19, 19, 11, 19, 3, 3, 3, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5] 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, 59]) total number of confs: 80 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457982872 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872 Building ZINC001457982872 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457982872 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 896) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC([C@H]2CCC[C@@H](C)C2)C1) `ZINC001457982872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457982872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457982872 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC([C@H]2CCC[C@@H](C)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.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', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 1, 2, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 3, 3, 17, 17, 17, 17, 3, 3, 3, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4] 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, 59]) total number of confs: 64 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 897) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC([C@H]2CCC[C@@H](C)C2)C1) `ZINC001457982872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457982872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457982872 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC([C@H]2CCC[C@@H](C)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.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', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 1, 2, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 5, 3, 3, 3, 19, 19, 11, 19, 3, 3, 3, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5] 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, 59]) total number of confs: 80 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457982872 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982872 Building ZINC001457982880 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457982880 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/898 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/898' -> `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]2CCC[C@@H](C)C2)C1) `ZINC001457982880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457982880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457982880 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC([C@@H]2CCC[C@@H](C)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.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', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 2, 4, 4, 7, 10, 10, 10, 10, 10, 10, 10, 10, 4, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4] 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, 59]) total number of confs: 52 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/899 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/899' -> `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]2CCC[C@@H](C)C2)C1) `ZINC001457982880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457982880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457982880 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC([C@@H]2CCC[C@@H](C)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.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', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 2, 4, 4, 7, 11, 11, 11, 11, 11, 11, 11, 11, 4, 3, 3, 3, 13, 13, 12, 13, 3, 3, 3, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4] 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, 59]) total number of confs: 48 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457982880 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880 Building ZINC001457982880 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457982880 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 898) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC([C@@H]2CCC[C@@H](C)C2)C1) `ZINC001457982880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457982880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457982880 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC([C@@H]2CCC[C@@H](C)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.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', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 2, 4, 4, 7, 10, 10, 10, 10, 10, 10, 10, 10, 4, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4] 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, 59]) total number of confs: 52 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 899) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC([C@@H]2CCC[C@@H](C)C2)C1) `ZINC001457982880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457982880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457982880 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC([C@@H]2CCC[C@@H](C)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.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', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 2, 4, 4, 7, 11, 11, 11, 11, 11, 11, 11, 11, 4, 3, 3, 3, 13, 13, 12, 13, 3, 3, 3, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4] 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, 59]) total number of confs: 48 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457982880 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982880 Building ZINC001457982890 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457982890 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/900 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/900' -> `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]2CCC[C@H](C)C2)C1) `ZINC001457982890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457982890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457982890 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC([C@@H]2CCC[C@H](C)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.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', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 1, 2, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 3, 3, 19, 19, 19, 19, 3, 3, 3, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4] 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, 59]) total number of confs: 75 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/901 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/901' -> `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]2CCC[C@H](C)C2)C1) `ZINC001457982890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457982890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457982890 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC([C@@H]2CCC[C@H](C)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.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', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 1, 2, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 4, 3, 3, 3, 18, 18, 15, 18, 3, 3, 3, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4] 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, 59]) total number of confs: 68 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457982890 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890 Building ZINC001457982890 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457982890 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 900) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC([C@@H]2CCC[C@H](C)C2)C1) `ZINC001457982890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457982890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457982890 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC([C@@H]2CCC[C@H](C)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.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', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 1, 2, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 3, 3, 19, 19, 19, 19, 3, 3, 3, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4] 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, 59]) total number of confs: 75 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 901) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC([C@@H]2CCC[C@H](C)C2)C1) `ZINC001457982890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457982890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457982890 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC([C@@H]2CCC[C@H](C)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.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', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 1, 2, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 4, 3, 3, 3, 18, 18, 15, 18, 3, 3, 3, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4] 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, 59]) total number of confs: 68 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457982890 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982890 Building ZINC001457982902 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457982902 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/902 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/902' -> `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]2CCC[C@H](C)C2)C1) `ZINC001457982902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457982902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457982902 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC([C@H]2CCC[C@H](C)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.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', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 1, 2, 4, 4, 7, 9, 9, 9, 9, 9, 9, 9, 9, 4, 2, 2, 2, 10, 10, 10, 10, 2, 2, 2, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4] 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, 59]) total number of confs: 43 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/903 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/903' -> `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]2CCC[C@H](C)C2)C1) `ZINC001457982902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457982902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457982902 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC([C@H]2CCC[C@H](C)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.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', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 2, 4, 4, 8, 9, 9, 9, 9, 9, 9, 9, 9, 4, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4] 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, 59]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457982902 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902 Building ZINC001457982902 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457982902 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 902) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC([C@H]2CCC[C@H](C)C2)C1) `ZINC001457982902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457982902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457982902 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC([C@H]2CCC[C@H](C)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.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', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 1, 2, 4, 4, 7, 9, 9, 9, 9, 9, 9, 9, 9, 4, 2, 2, 2, 10, 10, 10, 10, 2, 2, 2, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4] 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, 59]) total number of confs: 43 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 903) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC([C@H]2CCC[C@H](C)C2)C1) `ZINC001457982902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457982902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457982902 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC([C@H]2CCC[C@H](C)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.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', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 5, 5, 5, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 2, 4, 4, 8, 9, 9, 9, 9, 9, 9, 9, 9, 4, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4] 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, 59]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457982902 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457982902 Building ZINC001457989002 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457989002 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/904 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/904' -> `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)NCCCc1cccs1) `ZINC001457989002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457989002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457989002 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCc1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'C.2', 'C.2', 'C.2', 'S.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, 1, 1, 1, 1, 14, 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] 0 hydrogens need rotated 50 conformations in 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, 12, 16, 19, 19, 19, 19, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 11, 16, 16, 16, 16, 19, 19, 19] 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/905 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/905' -> `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)NCCCc1cccs1) `ZINC001457989002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457989002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457989002 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCc1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'C.2', 'C.2', 'C.2', 'S.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, 1, 1, 1, 1, 14, 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] 0 hydrogens need rotated 50 conformations in 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, 12, 16, 20, 20, 20, 20, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 11, 16, 16, 16, 16, 20, 20, 20] 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: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457989002 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002 Building ZINC001457989002 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457989002 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 904) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCc1cccs1) `ZINC001457989002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457989002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457989002 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCc1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'C.2', 'C.2', 'C.2', 'S.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, 1, 1, 1, 1, 14, 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] 0 hydrogens need rotated 50 conformations in 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, 12, 16, 19, 19, 19, 19, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 11, 16, 16, 16, 16, 19, 19, 19] 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 905) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCc1cccs1) `ZINC001457989002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457989002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457989002 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCc1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'C.2', 'C.2', 'C.2', 'S.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, 1, 1, 1, 1, 14, 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] 0 hydrogens need rotated 50 conformations in 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, 12, 16, 20, 20, 20, 20, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 11, 16, 16, 16, 16, 20, 20, 20] 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: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001457989002 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001457989002 Building ZINC001458024816 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458024816 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/906 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1c(c2ccc(F)cc2)nc2ccc(C(F)(F)F)cn21)[C@]([O-])([SiH3])c1ccccc1) `ZINC001458024816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458024816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001458024816 none O=C(NCc1c(c2ccc(F)cc2)nc2ccc(C(F)(F)F)cn21)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 6, 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, 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] 0 hydrogens 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, 6, 6, 32, 45, 45, 49, 49, 49, 49, 49, 49, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 4, 4, 1, 4, 4, 6, 32, 32, 49, 49, 49, 49, 45, 45, 45, 4, 4, 1, 4, 4] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/907 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/907' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1c(c2ccc(F)cc2)nc2ccc(C(F)(F)F)cn21)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001458024816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458024816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001458024816 none O=C(NCc1c(c2ccc(F)cc2)nc2ccc(C(F)(F)F)cn21)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 6, 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, 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] 0 hydrogens 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, 6, 6, 32, 45, 45, 49, 49, 49, 49, 49, 49, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 4, 4, 1, 4, 4, 6, 32, 32, 49, 49, 49, 49, 45, 45, 45, 4, 4, 1, 4, 4] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458024816 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816 Building ZINC001458024816 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458024816 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 906) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1c(c2ccc(F)cc2)nc2ccc(C(F)(F)F)cn21)[C@]([O-])([SiH3])c1ccccc1) `ZINC001458024816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458024816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001458024816 none O=C(NCc1c(c2ccc(F)cc2)nc2ccc(C(F)(F)F)cn21)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 6, 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, 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] 0 hydrogens 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, 6, 6, 32, 45, 45, 49, 49, 49, 49, 49, 49, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 4, 4, 1, 4, 4, 6, 32, 32, 49, 49, 49, 49, 45, 45, 45, 4, 4, 1, 4, 4] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 907) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1c(c2ccc(F)cc2)nc2ccc(C(F)(F)F)cn21)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001458024816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458024816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001458024816 none O=C(NCc1c(c2ccc(F)cc2)nc2ccc(C(F)(F)F)cn21)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 6, 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, 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] 0 hydrogens 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, 6, 6, 32, 45, 45, 49, 49, 49, 49, 49, 49, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 4, 4, 1, 4, 4, 6, 32, 32, 49, 49, 49, 49, 45, 45, 45, 4, 4, 1, 4, 4] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458024816 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458024816 Building ZINC001458035757 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458035757 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/908 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/908' -> `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)(C)[C@H]2CCC[C@H]21) `ZINC001458035757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458035757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001458035757 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C)(C)[C@H]2CCC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', '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, 5, 5, 5, 7, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 19, 19, 5, 19, 3, 3, 3, 11, 11, 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, 55, 56]) total number of confs: 70 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/909 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/909' -> `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)(C)[C@H]2CCC[C@H]21) `ZINC001458035757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458035757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001458035757 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C)(C)[C@H]2CCC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', '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, 5, 5, 5, 7, 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] dock 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 26, 26, 3, 26, 26, 26, 26, 26, 26, 3, 3, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 26, 26, 3, 26, 3, 3, 3, 9, 9, 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, 55, 56]) total number of confs: 76 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458035757 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757 Building ZINC001458035757 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458035757 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 908) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C)(C)[C@H]2CCC[C@H]21) `ZINC001458035757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458035757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001458035757 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C)(C)[C@H]2CCC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', '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, 5, 5, 5, 7, 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] dock 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] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 19, 19, 5, 19, 3, 3, 3, 11, 11, 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, 55, 56]) total number of confs: 70 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 909) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C)(C)[C@H]2CCC[C@H]21) `ZINC001458035757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458035757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001458035757 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C)(C)[C@H]2CCC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', '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, 5, 5, 5, 7, 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] dock 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 26, 26, 3, 26, 26, 26, 26, 26, 26, 3, 3, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 26, 26, 3, 26, 3, 3, 3, 9, 9, 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, 55, 56]) total number of confs: 76 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458035757 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458035757 Building ZINC001458037993 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458037993 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/910 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@H]1c1ccccc1C(F)(F)F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458037993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458037993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458037993 none O=C(N[C@@H]1CCC[C@H]1c1ccccc1C(F)(F)F)[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', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 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, 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] 0 hydrogens 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, 9, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 27, 27, 27, 27, 1, 1, 1, 8, 8, 8, 8, 10, 10, 8, 10, 10, 8, 4, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 8, 10, 10, 8, 10, 10, 8] 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]) total number of confs: 94 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/911 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/911' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@H]1c1ccccc1C(F)(F)F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458037993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458037993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458037993 none O=C(N[C@@H]1CCC[C@H]1c1ccccc1C(F)(F)F)[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', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 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, 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] 0 hydrogens need 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, 11, 24, 24, 24, 24, 24, 24, 24, 28, 28, 24, 28, 28, 28, 28, 28, 28, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 3, 24, 24, 24, 24, 24, 24, 28, 28, 24, 28, 6, 7, 7, 7, 7, 7, 6] 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]) total number of confs: 86 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458037993 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993 Building ZINC001458037993 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458037993 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 910) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1CCC[C@H]1c1ccccc1C(F)(F)F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458037993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458037993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458037993 none O=C(N[C@@H]1CCC[C@H]1c1ccccc1C(F)(F)F)[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', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 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, 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] 0 hydrogens 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, 9, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 27, 27, 27, 27, 1, 1, 1, 8, 8, 8, 8, 10, 10, 8, 10, 10, 8, 4, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 8, 10, 10, 8, 10, 10, 8] 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]) total number of confs: 94 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 911) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1CCC[C@H]1c1ccccc1C(F)(F)F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458037993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458037993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458037993 none O=C(N[C@@H]1CCC[C@H]1c1ccccc1C(F)(F)F)[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', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 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, 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] 0 hydrogens need 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, 11, 24, 24, 24, 24, 24, 24, 24, 28, 28, 24, 28, 28, 28, 28, 28, 28, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 3, 24, 24, 24, 24, 24, 24, 28, 28, 24, 28, 6, 7, 7, 7, 7, 7, 6] 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]) total number of confs: 86 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458037993 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037993 Building ZINC001458037995 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458037995 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/912 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC[C@H]1c1ccccc1C(F)(F)F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458037995.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458037995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458037995 none O=C(N[C@H]1CCC[C@H]1c1ccccc1C(F)(F)F)[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', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 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, 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] 0 hydrogens 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, 8, 22, 22, 22, 22, 22, 22, 22, 25, 25, 22, 25, 25, 25, 25, 25, 25, 1, 1, 1, 8, 8, 8, 8, 10, 10, 8, 10, 10, 8, 5, 22, 22, 22, 22, 22, 22, 25, 25, 25, 25, 8, 10, 10, 8, 10, 10, 8] 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]) total number of confs: 98 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/913 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/913' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC[C@H]1c1ccccc1C(F)(F)F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458037995.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458037995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458037995 none O=C(N[C@H]1CCC[C@H]1c1ccccc1C(F)(F)F)[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', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 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, 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] 0 hydrogens 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, 7, 20, 20, 20, 20, 20, 20, 20, 23, 23, 20, 23, 23, 23, 23, 23, 23, 1, 1, 1, 9, 9, 9, 9, 13, 13, 9, 13, 13, 9, 4, 20, 20, 20, 20, 20, 20, 23, 23, 23, 23, 9, 13, 13, 9, 13, 13, 9] 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]) total number of confs: 98 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458037995 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995 Building ZINC001458037995 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458037995 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 912) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@H]1CCC[C@H]1c1ccccc1C(F)(F)F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458037995.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458037995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458037995 none O=C(N[C@H]1CCC[C@H]1c1ccccc1C(F)(F)F)[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', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 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, 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] 0 hydrogens 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, 8, 22, 22, 22, 22, 22, 22, 22, 25, 25, 22, 25, 25, 25, 25, 25, 25, 1, 1, 1, 8, 8, 8, 8, 10, 10, 8, 10, 10, 8, 5, 22, 22, 22, 22, 22, 22, 25, 25, 25, 25, 8, 10, 10, 8, 10, 10, 8] 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]) total number of confs: 98 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 913) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@H]1CCC[C@H]1c1ccccc1C(F)(F)F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458037995.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458037995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458037995 none O=C(N[C@H]1CCC[C@H]1c1ccccc1C(F)(F)F)[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', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 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, 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] 0 hydrogens 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, 7, 20, 20, 20, 20, 20, 20, 20, 23, 23, 20, 23, 23, 23, 23, 23, 23, 1, 1, 1, 9, 9, 9, 9, 13, 13, 9, 13, 13, 9, 4, 20, 20, 20, 20, 20, 20, 23, 23, 23, 23, 9, 13, 13, 9, 13, 13, 9] 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]) total number of confs: 98 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458037995 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458037995 Building ZINC001458038000 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458038000 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/914 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC[C@@H]1c1ccccc1C(F)(F)F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458038000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458038000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458038000 none O=C(N[C@H]1CCC[C@@H]1c1ccccc1C(F)(F)F)[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', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 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, 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] 0 hydrogens need 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, 6, 21, 21, 21, 21, 21, 21, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 21, 21, 21, 21, 21, 21, 25, 25, 25, 25, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 66 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/915 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/915' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC[C@@H]1c1ccccc1C(F)(F)F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458038000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458038000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458038000 none O=C(N[C@H]1CCC[C@@H]1c1ccccc1C(F)(F)F)[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', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 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, 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] 0 hydrogens need 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, 26, 26, 26, 26, 26, 26, 26, 29, 29, 26, 29, 29, 29, 29, 29, 29, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 26, 26, 26, 26, 26, 26, 29, 29, 26, 29, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 82 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458038000 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000 Building ZINC001458038000 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458038000 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 914) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCC[C@@H]1c1ccccc1C(F)(F)F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458038000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458038000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458038000 none O=C(N[C@H]1CCC[C@@H]1c1ccccc1C(F)(F)F)[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', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 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, 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] 0 hydrogens need 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, 6, 21, 21, 21, 21, 21, 21, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 21, 21, 21, 21, 21, 21, 25, 25, 25, 25, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 66 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 915) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCC[C@@H]1c1ccccc1C(F)(F)F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458038000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458038000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458038000 none O=C(N[C@H]1CCC[C@@H]1c1ccccc1C(F)(F)F)[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', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 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, 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] 0 hydrogens need 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, 26, 26, 26, 26, 26, 26, 26, 29, 29, 26, 29, 29, 29, 29, 29, 29, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 26, 26, 26, 26, 26, 26, 29, 29, 26, 29, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 82 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458038000 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038000 Building ZINC001458038006 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458038006 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/916 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@@H]1c1ccccc1C(F)(F)F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458038006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458038006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458038006 none O=C(N[C@@H]1CCC[C@@H]1c1ccccc1C(F)(F)F)[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', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 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, 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] 0 hydrogens 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, 7, 20, 20, 20, 20, 20, 20, 20, 23, 23, 20, 23, 23, 23, 23, 23, 23, 1, 1, 1, 9, 9, 9, 9, 12, 12, 9, 12, 12, 9, 4, 20, 20, 20, 20, 20, 20, 23, 23, 20, 23, 9, 12, 12, 9, 12, 12, 9] 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]) total number of confs: 90 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/917 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/917' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@@H]1c1ccccc1C(F)(F)F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458038006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458038006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458038006 none O=C(N[C@@H]1CCC[C@@H]1c1ccccc1C(F)(F)F)[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', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 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, 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] 0 hydrogens 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, 8, 22, 22, 22, 22, 22, 22, 22, 25, 25, 22, 25, 25, 25, 25, 25, 25, 1, 1, 1, 8, 8, 8, 8, 10, 10, 8, 10, 10, 8, 5, 22, 22, 22, 22, 22, 22, 25, 25, 22, 25, 8, 10, 10, 8, 10, 10, 8] 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]) total number of confs: 92 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458038006 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006 Building ZINC001458038006 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458038006 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 916) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1CCC[C@@H]1c1ccccc1C(F)(F)F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458038006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458038006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458038006 none O=C(N[C@@H]1CCC[C@@H]1c1ccccc1C(F)(F)F)[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', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 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, 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] 0 hydrogens 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, 7, 20, 20, 20, 20, 20, 20, 20, 23, 23, 20, 23, 23, 23, 23, 23, 23, 1, 1, 1, 9, 9, 9, 9, 12, 12, 9, 12, 12, 9, 4, 20, 20, 20, 20, 20, 20, 23, 23, 20, 23, 9, 12, 12, 9, 12, 12, 9] 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]) total number of confs: 90 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 917) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1CCC[C@@H]1c1ccccc1C(F)(F)F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458038006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458038006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458038006 none O=C(N[C@@H]1CCC[C@@H]1c1ccccc1C(F)(F)F)[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', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 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, 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] 0 hydrogens 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, 8, 22, 22, 22, 22, 22, 22, 22, 25, 25, 22, 25, 25, 25, 25, 25, 25, 1, 1, 1, 8, 8, 8, 8, 10, 10, 8, 10, 10, 8, 5, 22, 22, 22, 22, 22, 22, 25, 25, 22, 25, 8, 10, 10, 8, 10, 10, 8] 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]) total number of confs: 92 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458038006 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458038006 Building ZINC001458047717 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458047717 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/918 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Br) `ZINC001458047717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458047717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001458047717 none CC(C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 16, 22, 22, 22, 22, 22, 22, 16, 16, 16, 16, 16, 16, 6, 9, 9, 22, 22, 22, 22] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/919 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/919' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Br) `ZINC001458047717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458047717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001458047717 none CC(C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 16, 22, 22, 21, 22, 22, 22, 16, 16, 16, 16, 16, 16, 6, 9, 9, 22, 22, 22, 22] 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458047717 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717 Building ZINC001458047717 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458047717 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 918) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Br) `ZINC001458047717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458047717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001458047717 none CC(C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 16, 22, 22, 22, 22, 22, 22, 16, 16, 16, 16, 16, 16, 6, 9, 9, 22, 22, 22, 22] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 919) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Br) `ZINC001458047717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458047717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001458047717 none CC(C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 16, 22, 22, 21, 22, 22, 22, 16, 16, 16, 16, 16, 16, 6, 9, 9, 22, 22, 22, 22] 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458047717 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458047717 Building ZINC001458068966 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458068966 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/920 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cc(Br)ccc1F)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458068966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458068966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001458068966 none C[C@H](Cc1cc(Br)ccc1F)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 17, 1, 1, 1, 15, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 10, 10, 27, 44, 44, 44, 38, 44, 44, 44, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 10, 10, 27, 27, 44, 27, 44, 2, 3, 1, 3] 50 rigid atoms, others: [13, 15, 16, 17] 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]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/921 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/921' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cc(Br)ccc1F)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458068966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458068966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001458068966 none C[C@H](Cc1cc(Br)ccc1F)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 17, 1, 1, 1, 15, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 46, 46, 40, 46, 46, 46, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 28, 28, 46, 28, 46, 3, 3, 1, 3] 50 rigid atoms, others: [13, 15, 16, 17] 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]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458068966 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966 Building ZINC001458068966 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458068966 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 920) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@H](Cc1cc(Br)ccc1F)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458068966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458068966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001458068966 none C[C@H](Cc1cc(Br)ccc1F)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 17, 1, 1, 1, 15, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 10, 10, 27, 44, 44, 44, 38, 44, 44, 44, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 10, 10, 27, 27, 44, 27, 44, 2, 3, 1, 3] 50 rigid atoms, others: [13, 15, 16, 17] 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]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 921) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@H](Cc1cc(Br)ccc1F)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458068966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458068966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001458068966 none C[C@H](Cc1cc(Br)ccc1F)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 17, 1, 1, 1, 15, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 46, 46, 40, 46, 46, 46, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 28, 28, 46, 28, 46, 3, 3, 1, 3] 50 rigid atoms, others: [13, 15, 16, 17] 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]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458068966 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458068966 Building ZINC001458069507 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458069507 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/922 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cc(Br)ccc1F)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458069507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458069507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001458069507 none C[C@@H](Cc1cc(Br)ccc1F)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 17, 1, 1, 1, 15, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 46, 46, 40, 46, 46, 46, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 28, 28, 46, 28, 46, 3, 3, 1, 3] 50 rigid atoms, others: [13, 15, 16, 17] 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]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/923 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/923' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cc(Br)ccc1F)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458069507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458069507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001458069507 none C[C@@H](Cc1cc(Br)ccc1F)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 17, 1, 1, 1, 15, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 10, 10, 27, 44, 44, 44, 38, 44, 44, 44, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 10, 10, 27, 27, 44, 38, 44, 2, 3, 1, 3] 50 rigid atoms, others: [13, 15, 16, 17] 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458069507 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507 Building ZINC001458069507 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458069507 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 922) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@H](Cc1cc(Br)ccc1F)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458069507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458069507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001458069507 none C[C@@H](Cc1cc(Br)ccc1F)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 17, 1, 1, 1, 15, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 46, 46, 40, 46, 46, 46, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 28, 28, 46, 28, 46, 3, 3, 1, 3] 50 rigid atoms, others: [13, 15, 16, 17] 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]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 923) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: C[C@@H](Cc1cc(Br)ccc1F)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458069507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458069507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001458069507 none C[C@@H](Cc1cc(Br)ccc1F)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 17, 1, 1, 1, 15, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 10, 10, 27, 44, 44, 44, 38, 44, 44, 44, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 10, 10, 27, 27, 44, 38, 44, 2, 3, 1, 3] 50 rigid atoms, others: [13, 15, 16, 17] 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458069507 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458069507 Building ZINC001458096642 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458096642 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/924 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C(=O)OC(C)(C)C)Cc2ccc(F)cc21) `ZINC001458096642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458096642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458096642 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C(=O)OC(C)(C)C)Cc2ccc(F)cc21 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 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, 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, 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] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 10, 10, 14, 14, 14, 14, 14, 14, 31, 31, 47, 47, 47, 47, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 47, 47, 47, 47, 47, 47, 47, 47, 47, 14, 14, 14, 14, 14] 48 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: 115 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/925 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/925' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C(=O)OC(C)(C)C)Cc2ccc(F)cc21) `ZINC001458096642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458096642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458096642 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C(=O)OC(C)(C)C)Cc2ccc(F)cc21 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 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, 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, 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] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 9, 9, 12, 12, 12, 12, 12, 12, 33, 33, 45, 45, 45, 45, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 45, 45, 45, 45, 45, 45, 45, 45, 45, 12, 12, 12, 12, 12] 49 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: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458096642 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642 Building ZINC001458096642 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458096642 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 924) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/924: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1C[C@H](C)N(C(=O)OC(C)(C)C)Cc2ccc(F)cc21) `ZINC001458096642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458096642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458096642 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C(=O)OC(C)(C)C)Cc2ccc(F)cc21 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 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, 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, 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] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 10, 10, 14, 14, 14, 14, 14, 14, 31, 31, 47, 47, 47, 47, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 47, 47, 47, 47, 47, 47, 47, 47, 47, 14, 14, 14, 14, 14] 48 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: 115 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 925) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1C[C@H](C)N(C(=O)OC(C)(C)C)Cc2ccc(F)cc21) `ZINC001458096642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458096642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458096642 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C(=O)OC(C)(C)C)Cc2ccc(F)cc21 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 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, 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, 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] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 9, 9, 12, 12, 12, 12, 12, 12, 33, 33, 45, 45, 45, 45, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 45, 45, 45, 45, 45, 45, 45, 45, 45, 12, 12, 12, 12, 12] 49 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: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458096642 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096642 Building ZINC001458096644 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458096644 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/926 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C(=O)OC(C)(C)C)Cc2ccc(F)cc21) `ZINC001458096644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458096644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458096644 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C(=O)OC(C)(C)C)Cc2ccc(F)cc21 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 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, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 14, 14, 14, 14, 14, 14, 32, 32, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14] 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: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/927 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/927' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C(=O)OC(C)(C)C)Cc2ccc(F)cc21) `ZINC001458096644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458096644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458096644 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C(=O)OC(C)(C)C)Cc2ccc(F)cc21 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 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, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 14, 14, 14, 14, 14, 14, 32, 32, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14] 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: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458096644 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644 Building ZINC001458096644 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458096644 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 926) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C(=O)OC(C)(C)C)Cc2ccc(F)cc21) `ZINC001458096644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458096644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458096644 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C(=O)OC(C)(C)C)Cc2ccc(F)cc21 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 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, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 14, 14, 14, 14, 14, 14, 32, 32, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14] 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: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 927) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C(=O)OC(C)(C)C)Cc2ccc(F)cc21) `ZINC001458096644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458096644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458096644 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C(=O)OC(C)(C)C)Cc2ccc(F)cc21 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 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, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 14, 14, 14, 14, 14, 14, 32, 32, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14] 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: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458096644 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458096644 Building ZINC001458101280 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458101280 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/928 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cccc(Br)c2)CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001458101280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458101280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458101280 none O=C(NCC1(c2cccc(Br)c2)CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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, 8, 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, 16, 23, 38, 38, 38, 38, 38, 38, 23, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 3, 11, 11, 38, 38, 38, 38, 23, 23, 23, 23, 23, 23, 23, 23, 7, 7] 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: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/929 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/929' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cccc(Br)c2)CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001458101280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458101280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458101280 none O=C(NCC1(c2cccc(Br)c2)CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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, 8, 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, 17, 27, 41, 41, 41, 41, 41, 41, 27, 27, 27, 27, 1, 1, 1, 6, 6, 6, 6, 6, 3, 11, 11, 41, 41, 41, 41, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6] 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: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458101280 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280 Building ZINC001458101280 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458101280 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 928) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCC1(c2cccc(Br)c2)CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001458101280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458101280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458101280 none O=C(NCC1(c2cccc(Br)c2)CCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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, 8, 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, 16, 23, 38, 38, 38, 38, 38, 38, 23, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 3, 11, 11, 38, 38, 38, 38, 23, 23, 23, 23, 23, 23, 23, 23, 7, 7] 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: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 929) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCC1(c2cccc(Br)c2)CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001458101280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458101280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458101280 none O=C(NCC1(c2cccc(Br)c2)CCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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, 8, 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, 17, 27, 41, 41, 41, 41, 41, 41, 27, 27, 27, 27, 1, 1, 1, 6, 6, 6, 6, 6, 3, 11, 11, 41, 41, 41, 41, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6] 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: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458101280 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458101280 Building ZINC001458186870 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458186870 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/930 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2ccc(Cl)cc2)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001458186870.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458186870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC001458186870 none O=C(Nc1nnc(c2ccc(Cl)cc2)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 11, 11, 21, 21, 21, 21, 37, 37, 34, 37, 37, 37, 21, 1, 1, 1, 12, 12, 12, 12, 12, 11, 37, 37, 37, 37, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 100 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/931 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/931' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2ccc(Cl)cc2)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001458186870.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458186870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC001458186870 none O=C(Nc1nnc(c2ccc(Cl)cc2)s1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 11, 11, 21, 21, 21, 21, 35, 35, 31, 31, 35, 35, 21, 1, 1, 1, 12, 12, 12, 12, 12, 11, 35, 35, 35, 35, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458186870 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870 Building ZINC001458186870 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458186870 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 930) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Nc1nnc(c2ccc(Cl)cc2)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001458186870.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458186870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC001458186870 none O=C(Nc1nnc(c2ccc(Cl)cc2)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 11, 11, 21, 21, 21, 21, 37, 37, 34, 37, 37, 37, 21, 1, 1, 1, 12, 12, 12, 12, 12, 11, 37, 37, 37, 37, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 100 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 931) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Nc1nnc(c2ccc(Cl)cc2)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001458186870.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458186870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC001458186870 none O=C(Nc1nnc(c2ccc(Cl)cc2)s1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 11, 11, 21, 21, 21, 21, 35, 35, 31, 31, 35, 35, 21, 1, 1, 1, 12, 12, 12, 12, 12, 11, 35, 35, 35, 35, 12, 12] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458186870 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458186870 Building ZINC001458234725 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458234725 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/932 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(Br)ccc1CCCNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458234725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458234725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001458234725 none COc1cc(Br)ccc1CCCNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 17, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 48, 48, 48, 24, 18, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 50, 50, 50, 48, 48, 48, 24, 24, 24, 24, 13, 13, 2, 2, 1, 2] 50 rigid atoms, others: [13, 15, 16, 17] 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]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/933 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/933' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(Br)ccc1CCCNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458234725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458234725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001458234725 none COc1cc(Br)ccc1CCCNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 17, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 48, 48, 48, 24, 18, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 50, 50, 50, 48, 48, 48, 24, 24, 24, 24, 13, 13, 2, 2, 1, 2] 50 rigid atoms, others: [13, 15, 16, 17] 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]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458234725 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725 Building ZINC001458234725 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458234725 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 932) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1cc(Br)ccc1CCCNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458234725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458234725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001458234725 none COc1cc(Br)ccc1CCCNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 17, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 48, 48, 48, 24, 18, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 50, 50, 50, 48, 48, 48, 24, 24, 24, 24, 13, 13, 2, 2, 1, 2] 50 rigid atoms, others: [13, 15, 16, 17] 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]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 933) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1cc(Br)ccc1CCCNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458234725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458234725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001458234725 none COc1cc(Br)ccc1CCCNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 17, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 48, 48, 48, 24, 18, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 50, 50, 50, 48, 48, 48, 24, 24, 24, 24, 13, 13, 2, 2, 1, 2] 50 rigid atoms, others: [13, 15, 16, 17] 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]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458234725 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458234725 Building ZINC001458244251 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458244251 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/934 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458244251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244251 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 5, 11, 18, 18, 18, 18, 18, 18, 18, 18, 38, 45, 45, 45, 45, 45, 18, 18, 18, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 18, 18, 18, 18, 18, 18, 18, 18, 38, 38, 45, 45, 45, 45, 45, 18, 18, 3, 1, 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, 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/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/935 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/935' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458244251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244251 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 5, 11, 18, 18, 18, 18, 18, 18, 18, 18, 38, 45, 45, 45, 45, 45, 18, 18, 18, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 18, 18, 18, 18, 18, 18, 18, 18, 38, 38, 45, 45, 45, 45, 45, 18, 18, 3, 1, 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, 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/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/936 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/936' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244251.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458244251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244251 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 13, 19, 19, 19, 19, 19, 19, 19, 19, 41, 46, 46, 45, 46, 46, 19, 19, 19, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 19, 19, 19, 19, 19, 19, 19, 19, 41, 41, 46, 46, 46, 46, 46, 19, 19, 3, 1, 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, 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/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/937 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/937' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244251.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458244251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244251 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 13, 19, 19, 19, 19, 19, 19, 19, 19, 41, 46, 46, 45, 46, 46, 19, 19, 19, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 19, 19, 19, 19, 19, 19, 19, 19, 41, 41, 46, 46, 46, 46, 46, 19, 19, 3, 1, 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, 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/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458244251 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 Building ZINC001458244251 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458244251 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 934) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458244251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244251 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 5, 11, 18, 18, 18, 18, 18, 18, 18, 18, 38, 45, 45, 45, 45, 45, 18, 18, 18, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 18, 18, 18, 18, 18, 18, 18, 18, 38, 38, 45, 45, 45, 45, 45, 18, 18, 3, 1, 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, 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/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 935) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458244251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244251 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 5, 11, 18, 18, 18, 18, 18, 18, 18, 18, 38, 45, 45, 45, 45, 45, 18, 18, 18, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 18, 18, 18, 18, 18, 18, 18, 18, 38, 38, 45, 45, 45, 45, 45, 18, 18, 3, 1, 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, 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/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 936) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/936: 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]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244251.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458244251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244251 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 13, 19, 19, 19, 19, 19, 19, 19, 19, 41, 46, 46, 45, 46, 46, 19, 19, 19, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 19, 19, 19, 19, 19, 19, 19, 19, 41, 41, 46, 46, 46, 46, 46, 19, 19, 3, 1, 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, 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/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 937) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/937: 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]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244251.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458244251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244251 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 13, 19, 19, 19, 19, 19, 19, 19, 19, 41, 46, 46, 45, 46, 46, 19, 19, 19, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 19, 19, 19, 19, 19, 19, 19, 19, 41, 41, 46, 46, 46, 46, 46, 19, 19, 3, 1, 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, 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/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458244251 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 Building ZINC001458244251 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458244251 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 934) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458244251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244251 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 5, 11, 18, 18, 18, 18, 18, 18, 18, 18, 38, 45, 45, 45, 45, 45, 18, 18, 18, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 18, 18, 18, 18, 18, 18, 18, 18, 38, 38, 45, 45, 45, 45, 45, 18, 18, 3, 1, 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, 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/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 935) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458244251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244251 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 5, 11, 18, 18, 18, 18, 18, 18, 18, 18, 38, 45, 45, 45, 45, 45, 18, 18, 18, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 18, 18, 18, 18, 18, 18, 18, 18, 38, 38, 45, 45, 45, 45, 45, 18, 18, 3, 1, 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, 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/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 936) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/936: 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]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244251.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458244251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244251 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 13, 19, 19, 19, 19, 19, 19, 19, 19, 41, 46, 46, 45, 46, 46, 19, 19, 19, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 19, 19, 19, 19, 19, 19, 19, 19, 41, 41, 46, 46, 46, 46, 46, 19, 19, 3, 1, 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, 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/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 937) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/937: 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]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244251.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458244251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244251 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 13, 19, 19, 19, 19, 19, 19, 19, 19, 41, 46, 46, 45, 46, 46, 19, 19, 19, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 19, 19, 19, 19, 19, 19, 19, 19, 41, 41, 46, 46, 46, 46, 46, 19, 19, 3, 1, 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, 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/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458244251 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 Building ZINC001458244251 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458244251 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 934) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458244251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244251 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 5, 11, 18, 18, 18, 18, 18, 18, 18, 18, 38, 45, 45, 45, 45, 45, 18, 18, 18, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 18, 18, 18, 18, 18, 18, 18, 18, 38, 38, 45, 45, 45, 45, 45, 18, 18, 3, 1, 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, 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/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 935) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458244251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244251 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 5, 11, 18, 18, 18, 18, 18, 18, 18, 18, 38, 45, 45, 45, 45, 45, 18, 18, 18, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 18, 18, 18, 18, 18, 18, 18, 18, 38, 38, 45, 45, 45, 45, 45, 18, 18, 3, 1, 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, 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/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 936) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/936: 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]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244251.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458244251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244251 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 13, 19, 19, 19, 19, 19, 19, 19, 19, 41, 46, 46, 45, 46, 46, 19, 19, 19, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 19, 19, 19, 19, 19, 19, 19, 19, 41, 41, 46, 46, 46, 46, 46, 19, 19, 3, 1, 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, 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/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 937) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/937: 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]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244251.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458244251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244251 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 13, 19, 19, 19, 19, 19, 19, 19, 19, 41, 46, 46, 45, 46, 46, 19, 19, 19, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 19, 19, 19, 19, 19, 19, 19, 19, 41, 41, 46, 46, 46, 46, 46, 19, 19, 3, 1, 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, 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/182395/xbh-8058088.34/working/building/ZINC001458244251 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458244251 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244251 Building ZINC001458244255 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458244255 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/938 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458244255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244255 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 13, 13, 13, 13, 31, 41, 41, 38, 41, 41, 13, 13, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 41, 41, 41, 41, 41, 13, 13, 3, 1, 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, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/939 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/939' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458244255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244255 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 13, 13, 13, 13, 31, 41, 41, 38, 41, 41, 13, 13, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 41, 41, 41, 41, 41, 13, 13, 3, 1, 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, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/940 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/940' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244255.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458244255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244255 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 39, 46, 46, 40, 46, 46, 16, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 16, 16, 16, 16, 16, 16, 16, 16, 39, 39, 46, 46, 46, 46, 46, 16, 16, 3, 1, 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, 50, 51, 52]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/941 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/941' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244255.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458244255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244255 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 39, 46, 46, 40, 46, 46, 16, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 16, 16, 16, 16, 16, 16, 16, 16, 39, 39, 46, 46, 46, 46, 46, 16, 16, 3, 1, 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, 50, 51, 52]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458244255 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 Building ZINC001458244255 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458244255 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 938) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458244255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244255 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 13, 13, 13, 13, 31, 41, 41, 38, 41, 41, 13, 13, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 41, 41, 41, 41, 41, 13, 13, 3, 1, 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, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 939) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458244255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244255 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 13, 13, 13, 13, 31, 41, 41, 38, 41, 41, 13, 13, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 41, 41, 41, 41, 41, 13, 13, 3, 1, 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, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 940) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/940: 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]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244255.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458244255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244255 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 39, 46, 46, 40, 46, 46, 16, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 16, 16, 16, 16, 16, 16, 16, 16, 39, 39, 46, 46, 46, 46, 46, 16, 16, 3, 1, 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, 50, 51, 52]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 941) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/941: 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]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244255.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458244255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244255 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 39, 46, 46, 40, 46, 46, 16, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 16, 16, 16, 16, 16, 16, 16, 16, 39, 39, 46, 46, 46, 46, 46, 16, 16, 3, 1, 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, 50, 51, 52]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458244255 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 Building ZINC001458244255 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458244255 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 938) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458244255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244255 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 13, 13, 13, 13, 31, 41, 41, 38, 41, 41, 13, 13, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 41, 41, 41, 41, 41, 13, 13, 3, 1, 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, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 939) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458244255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244255 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 13, 13, 13, 13, 31, 41, 41, 38, 41, 41, 13, 13, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 41, 41, 41, 41, 41, 13, 13, 3, 1, 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, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 940) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/940: 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]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244255.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458244255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244255 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 39, 46, 46, 40, 46, 46, 16, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 16, 16, 16, 16, 16, 16, 16, 16, 39, 39, 46, 46, 46, 46, 46, 16, 16, 3, 1, 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, 50, 51, 52]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 941) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/941: 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]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244255.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458244255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244255 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 39, 46, 46, 40, 46, 46, 16, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 16, 16, 16, 16, 16, 16, 16, 16, 39, 39, 46, 46, 46, 46, 46, 16, 16, 3, 1, 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, 50, 51, 52]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458244255 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 Building ZINC001458244255 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458244255 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 938) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458244255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244255 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 13, 13, 13, 13, 31, 41, 41, 38, 41, 41, 13, 13, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 41, 41, 41, 41, 41, 13, 13, 3, 1, 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, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 939) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458244255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244255 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 13, 13, 13, 13, 31, 41, 41, 38, 41, 41, 13, 13, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 41, 41, 41, 41, 41, 13, 13, 3, 1, 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, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 940) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/940: 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]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244255.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458244255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244255 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 39, 46, 46, 40, 46, 46, 16, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 16, 16, 16, 16, 16, 16, 16, 16, 39, 39, 46, 46, 46, 46, 46, 16, 16, 3, 1, 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, 50, 51, 52]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 941) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/941: 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]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244255.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458244255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244255 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 39, 46, 46, 40, 46, 46, 16, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 16, 16, 16, 16, 16, 16, 16, 16, 39, 39, 46, 46, 46, 46, 46, 16, 16, 3, 1, 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, 50, 51, 52]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458244255 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244255 Building ZINC001458244260 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458244260 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/942 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458244260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244260 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 45, 48, 48, 48, 48, 48, 23, 23, 23, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 23, 23, 23, 23, 23, 23, 23, 23, 45, 45, 48, 48, 48, 48, 48, 23, 23, 3, 1, 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, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/943 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/943' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458244260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244260 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 45, 48, 48, 48, 48, 48, 23, 23, 23, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 23, 23, 23, 23, 23, 23, 23, 23, 45, 45, 48, 48, 48, 48, 48, 23, 23, 3, 1, 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, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/944 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/944' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244260.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458244260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244260 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 42, 48, 48, 46, 48, 48, 21, 21, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 21, 21, 21, 21, 21, 21, 21, 21, 42, 42, 48, 48, 48, 48, 48, 21, 21, 3, 1, 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, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/945 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/945' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244260.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458244260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244260 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 42, 48, 48, 46, 48, 48, 21, 21, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 21, 21, 21, 21, 21, 21, 21, 21, 42, 42, 48, 48, 48, 48, 48, 21, 21, 3, 1, 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, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458244260 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 Building ZINC001458244260 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458244260 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 942) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458244260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244260 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 45, 48, 48, 48, 48, 48, 23, 23, 23, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 23, 23, 23, 23, 23, 23, 23, 23, 45, 45, 48, 48, 48, 48, 48, 23, 23, 3, 1, 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, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 943) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458244260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244260 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 45, 48, 48, 48, 48, 48, 23, 23, 23, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 23, 23, 23, 23, 23, 23, 23, 23, 45, 45, 48, 48, 48, 48, 48, 23, 23, 3, 1, 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, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 944) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/944: 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]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244260.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458244260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244260 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 42, 48, 48, 46, 48, 48, 21, 21, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 21, 21, 21, 21, 21, 21, 21, 21, 42, 42, 48, 48, 48, 48, 48, 21, 21, 3, 1, 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, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 945) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/945: 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]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244260.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458244260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244260 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 42, 48, 48, 46, 48, 48, 21, 21, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 21, 21, 21, 21, 21, 21, 21, 21, 42, 42, 48, 48, 48, 48, 48, 21, 21, 3, 1, 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, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458244260 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 Building ZINC001458244260 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458244260 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 942) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458244260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244260 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 45, 48, 48, 48, 48, 48, 23, 23, 23, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 23, 23, 23, 23, 23, 23, 23, 23, 45, 45, 48, 48, 48, 48, 48, 23, 23, 3, 1, 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, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 943) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458244260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244260 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 45, 48, 48, 48, 48, 48, 23, 23, 23, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 23, 23, 23, 23, 23, 23, 23, 23, 45, 45, 48, 48, 48, 48, 48, 23, 23, 3, 1, 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, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 944) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/944: 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]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244260.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458244260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244260 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 42, 48, 48, 46, 48, 48, 21, 21, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 21, 21, 21, 21, 21, 21, 21, 21, 42, 42, 48, 48, 48, 48, 48, 21, 21, 3, 1, 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, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 945) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/945: 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]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244260.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458244260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244260 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 42, 48, 48, 46, 48, 48, 21, 21, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 21, 21, 21, 21, 21, 21, 21, 21, 42, 42, 48, 48, 48, 48, 48, 21, 21, 3, 1, 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, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458244260 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 Building ZINC001458244260 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458244260 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 942) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458244260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244260 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 45, 48, 48, 48, 48, 48, 23, 23, 23, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 23, 23, 23, 23, 23, 23, 23, 23, 45, 45, 48, 48, 48, 48, 48, 23, 23, 3, 1, 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, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 943) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458244260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244260 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 45, 48, 48, 48, 48, 48, 23, 23, 23, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 23, 23, 23, 23, 23, 23, 23, 23, 45, 45, 48, 48, 48, 48, 48, 23, 23, 3, 1, 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, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 944) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/944: 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]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244260.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458244260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244260 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 42, 48, 48, 46, 48, 48, 21, 21, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 21, 21, 21, 21, 21, 21, 21, 21, 42, 42, 48, 48, 48, 48, 48, 21, 21, 3, 1, 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, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 945) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/945: 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]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244260.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458244260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244260 none O=C(N[C@@H]1CCC[C@@H]2CN(Cc3ccccc3)C[C@@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [2, 1, 2, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 42, 48, 48, 46, 48, 48, 21, 21, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 21, 21, 21, 21, 21, 21, 21, 21, 42, 42, 48, 48, 48, 48, 48, 21, 21, 3, 1, 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, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458244260 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244260 Building ZINC001458244265 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458244265 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/946 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458244265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244265 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 41, 48, 48, 41, 48, 48, 18, 18, 18, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 41, 41, 48, 48, 43, 48, 48, 18, 18, 3, 1, 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, 50, 51, 52]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/947 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/947' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458244265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244265 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 41, 48, 48, 41, 48, 48, 18, 18, 18, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 41, 41, 48, 48, 43, 48, 48, 18, 18, 3, 1, 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, 50, 51, 52]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/948 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/948' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244265.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458244265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244265 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 44, 48, 48, 44, 48, 48, 20, 20, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 44, 44, 48, 48, 44, 48, 48, 20, 20, 3, 1, 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, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/949 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/949' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244265.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458244265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244265 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 44, 48, 48, 44, 48, 48, 20, 20, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 44, 44, 48, 48, 44, 48, 48, 20, 20, 3, 1, 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, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458244265 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 Building ZINC001458244265 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458244265 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 946) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458244265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244265 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 41, 48, 48, 41, 48, 48, 18, 18, 18, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 41, 41, 48, 48, 43, 48, 48, 18, 18, 3, 1, 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, 50, 51, 52]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 947) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458244265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244265 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 41, 48, 48, 41, 48, 48, 18, 18, 18, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 41, 41, 48, 48, 43, 48, 48, 18, 18, 3, 1, 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, 50, 51, 52]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 948) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/948: 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]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244265.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458244265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244265 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 44, 48, 48, 44, 48, 48, 20, 20, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 44, 44, 48, 48, 44, 48, 48, 20, 20, 3, 1, 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, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 949) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/949: 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]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244265.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458244265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244265 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 44, 48, 48, 44, 48, 48, 20, 20, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 44, 44, 48, 48, 44, 48, 48, 20, 20, 3, 1, 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, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458244265 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 Building ZINC001458244265 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458244265 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 946) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458244265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244265 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 41, 48, 48, 41, 48, 48, 18, 18, 18, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 41, 41, 48, 48, 43, 48, 48, 18, 18, 3, 1, 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, 50, 51, 52]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 947) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458244265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244265 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 41, 48, 48, 41, 48, 48, 18, 18, 18, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 41, 41, 48, 48, 43, 48, 48, 18, 18, 3, 1, 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, 50, 51, 52]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 948) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/948: 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]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244265.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458244265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244265 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 44, 48, 48, 44, 48, 48, 20, 20, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 44, 44, 48, 48, 44, 48, 48, 20, 20, 3, 1, 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, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 949) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/949: 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]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244265.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458244265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244265 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 44, 48, 48, 44, 48, 48, 20, 20, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 44, 44, 48, 48, 44, 48, 48, 20, 20, 3, 1, 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, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458244265 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 Building ZINC001458244265 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458244265 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 946) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458244265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244265 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 41, 48, 48, 41, 48, 48, 18, 18, 18, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 41, 41, 48, 48, 43, 48, 48, 18, 18, 3, 1, 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, 50, 51, 52]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 947) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458244265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244265 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 41, 48, 48, 41, 48, 48, 18, 18, 18, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 41, 41, 48, 48, 43, 48, 48, 18, 18, 3, 1, 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, 50, 51, 52]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 948) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/948: 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]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244265.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458244265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/2/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244265 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 44, 48, 48, 44, 48, 48, 20, 20, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 44, 44, 48, 48, 44, 48, 48, 20, 20, 3, 1, 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, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 949) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/949: 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]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458244265.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458244265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/3/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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458244265 none O=C(N[C@@H]1CCC[C@H]2CN(Cc3ccccc3)C[C@H]21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', '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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 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: [3, 1, 3, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 44, 48, 48, 44, 48, 48, 20, 20, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 44, 44, 48, 48, 44, 48, 48, 20, 20, 3, 1, 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, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458244265 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458244265 Building ZINC001458252508 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458252508 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/950 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)ccc1Sc1ccccc1) `ZINC001458252508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458252508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458252508 none CCOC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)ccc1Sc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 14, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 8, 29, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 8, 8, 25, 27, 27, 26, 27, 27, 30, 30, 30, 30, 30, 8, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 27, 27, 26, 27, 27] 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: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/951 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/951' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)ccc1Sc1ccccc1) `ZINC001458252508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458252508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458252508 none CCOC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)ccc1Sc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 14, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 8, 31, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 8, 8, 25, 28, 28, 25, 28, 28, 32, 32, 32, 32, 32, 8, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 28, 28, 25, 28, 28] 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: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458252508 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508 Building ZINC001458252508 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458252508 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 950) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCOC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)ccc1Sc1ccccc1) `ZINC001458252508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458252508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458252508 none CCOC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)ccc1Sc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 14, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 8, 29, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 8, 8, 25, 27, 27, 26, 27, 27, 30, 30, 30, 30, 30, 8, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 27, 27, 26, 27, 27] 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: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 951) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCOC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)ccc1Sc1ccccc1) `ZINC001458252508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458252508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458252508 none CCOC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)ccc1Sc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 14, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 8, 31, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 8, 8, 25, 28, 28, 25, 28, 28, 32, 32, 32, 32, 32, 8, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 28, 28, 25, 28, 28] 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: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458252508 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458252508 Building ZINC001458257499 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458257499 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/952 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(CC(F)F)c1c(C)cc(Br)cc1C) `ZINC001458257499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458257499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001458257499 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(CC(F)F)c1c(C)cc(Br)cc1C 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', 'F', 'F', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 1, 1, 5, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 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] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 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, 6, 7, 7, 4, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 6, 6, 6, 6, 6, 6, 6, 6] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 33 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/953 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/953' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(CC(F)F)c1c(C)cc(Br)cc1C) `ZINC001458257499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458257499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001458257499 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(CC(F)F)c1c(C)cc(Br)cc1C 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', 'F', 'F', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 1, 1, 5, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 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] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 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, 6, 7, 7, 4, 6, 6, 6, 4, 4, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 6, 6, 6, 6, 6, 6, 6, 6] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 39 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458257499 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499 Building ZINC001458257499 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458257499 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 952) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(CC(F)F)c1c(C)cc(Br)cc1C) `ZINC001458257499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458257499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001458257499 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(CC(F)F)c1c(C)cc(Br)cc1C 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', 'F', 'F', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 1, 1, 5, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 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] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 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, 6, 7, 7, 4, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 6, 6, 6, 6, 6, 6, 6, 6] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 33 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 953) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(CC(F)F)c1c(C)cc(Br)cc1C) `ZINC001458257499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458257499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001458257499 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(CC(F)F)c1c(C)cc(Br)cc1C 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', 'F', 'F', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 1, 1, 5, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 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] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 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, 6, 7, 7, 4, 6, 6, 6, 4, 4, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 6, 6, 6, 6, 6, 6, 6, 6] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 39 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458257499 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257499 Building ZINC001458257549 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458257549 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/954 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001458257549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458257549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458257549 none O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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] 0 hydrogens need 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, 14, 14, 14, 14, 14, 26, 40, 40, 40, 26, 40, 40, 40, 14, 14, 1, 1, 1, 6, 6, 6, 6, 6, 3, 14, 14, 14, 14, 26, 26, 40, 26, 40, 14, 14, 14, 14, 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]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/955 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/955' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001458257549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458257549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458257549 none O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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] 0 hydrogens need 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, 14, 14, 14, 14, 14, 28, 41, 41, 41, 32, 41, 41, 41, 14, 14, 1, 1, 1, 6, 6, 6, 6, 6, 3, 14, 14, 14, 14, 28, 28, 41, 36, 41, 14, 14, 14, 14, 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]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/956 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/956' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001458257549.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458257549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/2/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 46 natoms 45 natoms 44 natoms 43 names: ZINC001458257549 none O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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] 0 hydrogens need 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, 14, 14, 14, 14, 14, 27, 40, 40, 40, 34, 40, 40, 40, 14, 14, 1, 1, 1, 6, 6, 6, 6, 6, 3, 14, 14, 14, 14, 27, 27, 40, 40, 40, 14, 14, 14, 14, 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/957 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/957' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001458257549.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458257549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/3/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 46 natoms 45 natoms 44 natoms 43 names: ZINC001458257549 none O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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] 0 hydrogens need 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, 14, 14, 14, 14, 14, 27, 40, 40, 40, 27, 40, 40, 40, 14, 14, 1, 1, 1, 5, 5, 5, 5, 5, 3, 14, 14, 14, 14, 27, 27, 40, 34, 40, 14, 14, 14, 14, 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458257549 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 Building ZINC001458257549 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458257549 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 954) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001458257549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458257549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458257549 none O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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] 0 hydrogens need 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, 14, 14, 14, 14, 14, 26, 40, 40, 40, 26, 40, 40, 40, 14, 14, 1, 1, 1, 6, 6, 6, 6, 6, 3, 14, 14, 14, 14, 26, 26, 40, 26, 40, 14, 14, 14, 14, 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]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 955) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001458257549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458257549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458257549 none O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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] 0 hydrogens need 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, 14, 14, 14, 14, 14, 28, 41, 41, 41, 32, 41, 41, 41, 14, 14, 1, 1, 1, 6, 6, 6, 6, 6, 3, 14, 14, 14, 14, 28, 28, 41, 36, 41, 14, 14, 14, 14, 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]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 956) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/956: 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]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001458257549.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458257549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/2/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 46 natoms 45 natoms 44 natoms 43 names: ZINC001458257549 none O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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] 0 hydrogens need 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, 14, 14, 14, 14, 14, 27, 40, 40, 40, 34, 40, 40, 40, 14, 14, 1, 1, 1, 6, 6, 6, 6, 6, 3, 14, 14, 14, 14, 27, 27, 40, 40, 40, 14, 14, 14, 14, 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 957) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/957: 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]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001458257549.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458257549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/3/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 46 natoms 45 natoms 44 natoms 43 names: ZINC001458257549 none O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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] 0 hydrogens need 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, 14, 14, 14, 14, 14, 27, 40, 40, 40, 27, 40, 40, 40, 14, 14, 1, 1, 1, 5, 5, 5, 5, 5, 3, 14, 14, 14, 14, 27, 27, 40, 34, 40, 14, 14, 14, 14, 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458257549 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 Building ZINC001458257549 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458257549 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 954) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001458257549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458257549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458257549 none O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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] 0 hydrogens need 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, 14, 14, 14, 14, 14, 26, 40, 40, 40, 26, 40, 40, 40, 14, 14, 1, 1, 1, 6, 6, 6, 6, 6, 3, 14, 14, 14, 14, 26, 26, 40, 26, 40, 14, 14, 14, 14, 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]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 955) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001458257549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458257549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458257549 none O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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] 0 hydrogens need 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, 14, 14, 14, 14, 14, 28, 41, 41, 41, 32, 41, 41, 41, 14, 14, 1, 1, 1, 6, 6, 6, 6, 6, 3, 14, 14, 14, 14, 28, 28, 41, 36, 41, 14, 14, 14, 14, 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]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 956) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/956: 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]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001458257549.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458257549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/2/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 46 natoms 45 natoms 44 natoms 43 names: ZINC001458257549 none O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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] 0 hydrogens need 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, 14, 14, 14, 14, 14, 27, 40, 40, 40, 34, 40, 40, 40, 14, 14, 1, 1, 1, 6, 6, 6, 6, 6, 3, 14, 14, 14, 14, 27, 27, 40, 40, 40, 14, 14, 14, 14, 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 957) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/957: 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]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001458257549.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458257549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/3/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 46 natoms 45 natoms 44 natoms 43 names: ZINC001458257549 none O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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] 0 hydrogens need 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, 14, 14, 14, 14, 14, 27, 40, 40, 40, 27, 40, 40, 40, 14, 14, 1, 1, 1, 5, 5, 5, 5, 5, 3, 14, 14, 14, 14, 27, 27, 40, 34, 40, 14, 14, 14, 14, 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458257549 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 Building ZINC001458257549 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458257549 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 954) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001458257549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458257549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458257549 none O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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] 0 hydrogens need 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, 14, 14, 14, 14, 14, 26, 40, 40, 40, 26, 40, 40, 40, 14, 14, 1, 1, 1, 6, 6, 6, 6, 6, 3, 14, 14, 14, 14, 26, 26, 40, 26, 40, 14, 14, 14, 14, 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]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 955) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001458257549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458257549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458257549 none O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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] 0 hydrogens need 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, 14, 14, 14, 14, 14, 28, 41, 41, 41, 32, 41, 41, 41, 14, 14, 1, 1, 1, 6, 6, 6, 6, 6, 3, 14, 14, 14, 14, 28, 28, 41, 36, 41, 14, 14, 14, 14, 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]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `2' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/2 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 2 (index: 956) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/956: 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]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001458257549.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458257549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/2/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 46 natoms 45 natoms 44 natoms 43 names: ZINC001458257549 none O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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] 0 hydrogens need 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, 14, 14, 14, 14, 14, 27, 40, 40, 40, 34, 40, 40, 40, 14, 14, 1, 1, 1, 6, 6, 6, 6, 6, 3, 14, 14, 14, 14, 27, 27, 40, 40, 40, 14, 14, 14, 14, 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `3' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/3 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 3 (index: 957) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/957: 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]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001458257549.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458257549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/3/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 46 natoms 45 natoms 44 natoms 43 names: ZINC001458257549 none O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 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] 0 hydrogens need 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, 14, 14, 14, 14, 14, 27, 40, 40, 40, 27, 40, 40, 40, 14, 14, 1, 1, 1, 5, 5, 5, 5, 5, 3, 14, 14, 14, 14, 27, 27, 40, 34, 40, 14, 14, 14, 14, 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458257549 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/0.* 3: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/3.* 2: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549/2.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458257549 Building ZINC001458271923 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458271923 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/958 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(Sc2ccc(F)cc2)cc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458271923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458271923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001458271923 none O=C(NCc1ccc(Sc2ccc(F)cc2)cc1)[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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 11, 15, 15, 11, 11, 48, 48, 48, 48, 48, 48, 48, 15, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 11, 11, 15, 15, 48, 48, 48, 48, 15, 15, 4, 4, 4, 4, 4, 4, 4] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/959 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/959' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(Sc2ccc(F)cc2)cc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458271923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458271923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001458271923 none O=C(NCc1ccc(Sc2ccc(F)cc2)cc1)[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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 11, 16, 16, 11, 12, 49, 49, 49, 49, 49, 49, 49, 16, 16, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 11, 11, 16, 16, 49, 49, 49, 49, 16, 16, 3, 3, 3, 3, 3, 3, 3] 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458271923 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923 Building ZINC001458271923 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458271923 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 958) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NCc1ccc(Sc2ccc(F)cc2)cc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458271923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458271923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001458271923 none O=C(NCc1ccc(Sc2ccc(F)cc2)cc1)[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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 11, 15, 15, 11, 11, 48, 48, 48, 48, 48, 48, 48, 15, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 11, 11, 15, 15, 48, 48, 48, 48, 15, 15, 4, 4, 4, 4, 4, 4, 4] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 959) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NCc1ccc(Sc2ccc(F)cc2)cc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458271923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458271923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001458271923 none O=C(NCc1ccc(Sc2ccc(F)cc2)cc1)[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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 11, 16, 16, 11, 12, 49, 49, 49, 49, 49, 49, 49, 16, 16, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 11, 11, 16, 16, 49, 49, 49, 49, 16, 16, 3, 3, 3, 3, 3, 3, 3] 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458271923 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458271923 Building ZINC001458316948 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458316948 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/960 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F) `ZINC001458316948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458316948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458316948 none Cc1nn(c2ccccc2)c(C)c1[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)C(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', '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.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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 15, 15, 15, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 45, 45, 45, 45, 45, 25, 25, 9, 5, 9, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 25, 25, 25, 45, 45, 45, 45, 45, 25, 25, 25, 5, 4, 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, 48, 49]) total number of confs: 102 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/961 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/961' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F) `ZINC001458316948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458316948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458316948 none Cc1nn(c2ccccc2)c(C)c1[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)C(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', '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.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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 15, 15, 15, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 42, 42, 42, 42, 42, 25, 25, 9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 25, 25, 25, 42, 42, 42, 42, 42, 25, 25, 25, 5, 3, 3, 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]) total number of confs: 96 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458316948 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948 Building ZINC001458316948 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458316948 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 960) grep: /scratch/xiaobo/182395/xbh-8058088.34/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@H](NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F) `ZINC001458316948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458316948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458316948 none Cc1nn(c2ccccc2)c(C)c1[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)C(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', '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.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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 15, 15, 15, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 45, 45, 45, 45, 45, 25, 25, 9, 5, 9, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 25, 25, 25, 45, 45, 45, 45, 45, 25, 25, 25, 5, 4, 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, 48, 49]) total number of confs: 102 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 961) grep: /scratch/xiaobo/182395/xbh-8058088.34/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@H](NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F) `ZINC001458316948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458316948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458316948 none Cc1nn(c2ccccc2)c(C)c1[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)C(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', '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.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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 15, 15, 15, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 42, 42, 42, 42, 42, 25, 25, 9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 25, 25, 25, 42, 42, 42, 42, 42, 25, 25, 25, 5, 3, 3, 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]) total number of confs: 96 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458316948 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458316948 Building ZINC001458317085 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458317085 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/962 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F) `ZINC001458317085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458317085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458317085 none Cc1nn(c2ccccc2)c(C)c1[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)C(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', '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.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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 15, 15, 15, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 43, 43, 25, 43, 43, 25, 25, 9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 25, 25, 25, 43, 43, 25, 43, 43, 25, 25, 25, 5, 3, 3, 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]) total number of confs: 152 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/963 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/963' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F) `ZINC001458317085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458317085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458317085 none Cc1nn(c2ccccc2)c(C)c1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)C(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', '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.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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 15, 15, 15, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 44, 24, 44, 44, 24, 24, 9, 5, 9, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 24, 24, 24, 44, 44, 24, 44, 44, 24, 24, 24, 5, 4, 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, 48, 49]) total number of confs: 161 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458317085 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085 Building ZINC001458317085 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458317085 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 962) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/962: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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@@H](NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F) `ZINC001458317085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458317085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458317085 none Cc1nn(c2ccccc2)c(C)c1[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)C(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', '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.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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 15, 15, 15, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 43, 43, 25, 43, 43, 25, 25, 9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 25, 25, 25, 43, 43, 25, 43, 43, 25, 25, 25, 5, 3, 3, 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]) total number of confs: 152 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 963) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/963: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F) `ZINC001458317085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458317085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458317085 none Cc1nn(c2ccccc2)c(C)c1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)C(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', '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.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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 15, 15, 15, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 44, 24, 44, 44, 24, 24, 9, 5, 9, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 24, 24, 24, 44, 44, 24, 44, 44, 24, 24, 24, 5, 4, 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, 48, 49]) total number of confs: 161 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458317085 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458317085 Building ZINC001458347981 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458347981 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/964 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc(C(F)(F)F)c1) `ZINC001458347981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458347981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458347981 none CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc(C(F)(F)F)c1 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.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.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', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 19, 23, 8, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 19, 19, 9, 19, 19, 19, 19, 19, 19, 24, 24, 24, 24, 24, 23, 23, 23, 23, 23, 8, 8, 8, 8, 2, 2, 2, 2, 19, 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]) total number of confs: 169 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/965 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/965' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc(C(F)(F)F)c1) `ZINC001458347981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458347981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458347981 none CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc(C(F)(F)F)c1 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.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.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', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 22, 25, 8, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 21, 21, 5, 21, 21, 21, 21, 21, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 2, 2, 2, 2, 21, 21, 8, 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, 47, 48, 49, 50]) total number of confs: 161 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458347981 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981 Building ZINC001458347981 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458347981 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 964) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc(C(F)(F)F)c1) `ZINC001458347981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458347981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458347981 none CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc(C(F)(F)F)c1 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.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.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', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 19, 23, 8, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 19, 19, 9, 19, 19, 19, 19, 19, 19, 24, 24, 24, 24, 24, 23, 23, 23, 23, 23, 8, 8, 8, 8, 2, 2, 2, 2, 19, 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]) total number of confs: 169 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 965) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc(C(F)(F)F)c1) `ZINC001458347981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458347981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458347981 none CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc(C(F)(F)F)c1 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.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.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', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 22, 25, 8, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 21, 21, 5, 21, 21, 21, 21, 21, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 2, 2, 2, 2, 21, 21, 8, 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, 47, 48, 49, 50]) total number of confs: 161 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458347981 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458347981 Building ZINC001458395315 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458395315 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/966 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@H]2CC(C)(C)OC2(C)C)cc1Cl) `ZINC001458395315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458395315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458395315 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@H]2CC(C)(C)OC2(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 12, 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] 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 5, 10, 12, 12, 10, 12, 12, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 13, 13, 13, 6, 6, 10, 10, 12, 12, 10, 12, 12, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 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, 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: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/967 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/967' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@H]2CC(C)(C)OC2(C)C)cc1Cl) `ZINC001458395315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458395315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458395315 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@H]2CC(C)(C)OC2(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 12, 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] 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 4, 6, 12, 15, 15, 12, 15, 15, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 10, 10, 10, 6, 6, 12, 12, 15, 15, 12, 15, 15, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 104 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458395315 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315 Building ZINC001458395315 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458395315 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 966) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/966: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Cc2ccccc2)[C@H]2CC(C)(C)OC2(C)C)cc1Cl) `ZINC001458395315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458395315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458395315 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@H]2CC(C)(C)OC2(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 12, 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] 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 5, 10, 12, 12, 10, 12, 12, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 13, 13, 13, 6, 6, 10, 10, 12, 12, 10, 12, 12, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 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, 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: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 967) grep: /scratch/xiaobo/182395/xbh-8058088.34/working/3D/967: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Cc2ccccc2)[C@H]2CC(C)(C)OC2(C)C)cc1Cl) `ZINC001458395315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458395315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458395315 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@H]2CC(C)(C)OC2(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 12, 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] 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 4, 6, 12, 15, 15, 12, 15, 15, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 10, 10, 10, 6, 6, 12, 12, 15, 15, 12, 15, 15, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 104 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458395315 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395315 Building ZINC001458395322 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458395322 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/968 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@@H]2CC(C)(C)OC2(C)C)cc1Cl) `ZINC001458395322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458395322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458395322 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@@H]2CC(C)(C)OC2(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 12, 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] 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 4, 6, 12, 15, 15, 12, 15, 15, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 10, 10, 10, 6, 6, 12, 12, 15, 15, 12, 15, 15, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 104 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/969 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/969' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@@H]2CC(C)(C)OC2(C)C)cc1Cl) `ZINC001458395322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458395322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458395322 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@@H]2CC(C)(C)OC2(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 12, 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] 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 5, 10, 12, 12, 10, 12, 12, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 13, 13, 13, 6, 6, 10, 10, 12, 12, 10, 12, 12, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 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, 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: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458395322 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322 Building ZINC001458395322 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458395322 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 968) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@@H]2CC(C)(C)OC2(C)C)cc1Cl) `ZINC001458395322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458395322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458395322 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@@H]2CC(C)(C)OC2(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 12, 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] 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 4, 6, 12, 15, 15, 12, 15, 15, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 10, 10, 10, 6, 6, 12, 12, 15, 15, 12, 15, 15, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 104 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 969) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@@H]2CC(C)(C)OC2(C)C)cc1Cl) `ZINC001458395322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458395322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458395322 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)[C@@H]2CC(C)(C)OC2(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 12, 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] 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 5, 10, 12, 12, 10, 12, 12, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 13, 13, 13, 6, 6, 10, 10, 12, 12, 10, 12, 12, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 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, 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: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458395322 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458395322 Building ZINC001458478201 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458478201 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/970 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1Cc1ccc(SC(F)(F)F)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001458478201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458478201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458478201 none O=C(Nc1ccnn1Cc1ccc(SC(F)(F)F)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 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, 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: [1, 1, 1, 2, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 31, 32, 32, 32, 9, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 20, 21, 22] set([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: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/971 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/971' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1Cc1ccc(SC(F)(F)F)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001458478201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458478201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458478201 none O=C(Nc1ccnn1Cc1ccc(SC(F)(F)F)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 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, 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: [1, 1, 1, 2, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 30, 31, 31, 31, 9, 9, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 20, 21, 22] set([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: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458478201 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201 Building ZINC001458478201 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458478201 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 970) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(Nc1ccnn1Cc1ccc(SC(F)(F)F)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001458478201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458478201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458478201 none O=C(Nc1ccnn1Cc1ccc(SC(F)(F)F)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 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, 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: [1, 1, 1, 2, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 31, 32, 32, 32, 9, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 20, 21, 22] set([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: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 971) grep: /scratch/xiaobo/182395/xbh-8058088.34/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(Nc1ccnn1Cc1ccc(SC(F)(F)F)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001458478201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458478201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458478201 none O=C(Nc1ccnn1Cc1ccc(SC(F)(F)F)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 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, 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: [1, 1, 1, 2, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 30, 31, 31, 31, 9, 9, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 20, 21, 22] set([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: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458478201 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458478201 Building ZINC001458567748 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458567748 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/972 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)c1) `ZINC001458567748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458567748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458567748 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 15, 15, 16, 16, 16, 16, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 6, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 39] 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, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/973 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/973' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)c1) `ZINC001458567748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458567748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458567748 none Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 3, 3, 4, 11, 15, 15, 16, 16, 16, 16, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 2, 4, 4, 2, 4, 4, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 8, 8, 8, 8, 8, 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, 59]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458567748 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748 Building ZINC001458567748 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458567748 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 972) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)c1) `ZINC001458567748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458567748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458567748 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 15, 15, 16, 16, 16, 16, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 6, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 39] 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, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 973) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)c1) `ZINC001458567748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458567748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458567748 none Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 3, 3, 4, 11, 15, 15, 16, 16, 16, 16, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 2, 4, 4, 2, 4, 4, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 8, 8, 8, 8, 8, 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, 59]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458567748 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567748 Building ZINC001458567749 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458567749 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/974 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)c1) `ZINC001458567749.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458567749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458567749 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 3, 3, 4, 11, 16, 16, 16, 16, 16, 16, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 2, 4, 4, 2, 4, 4, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 8, 8, 8, 8, 8, 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, 59]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/975 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/975' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)c1) `ZINC001458567749.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458567749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458567749 none Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 15, 15, 16, 16, 16, 16, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 6, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 39] 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, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458567749 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749 Building ZINC001458567749 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458567749 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 974) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)c1) `ZINC001458567749.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458567749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458567749 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 3, 3, 4, 11, 16, 16, 16, 16, 16, 16, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 2, 4, 4, 2, 4, 4, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 8, 8, 8, 8, 8, 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, 59]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 975) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)c1) `ZINC001458567749.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458567749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458567749 none Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 15, 15, 16, 16, 16, 16, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 6, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 39] 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, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458567749 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458567749 Building ZINC001458629459 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458629459 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/976 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Cl)cc2Cl)CCCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458629459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458629459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001458629459 none O=C(NCC1(c2ccc(Cl)cc2Cl)CCCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens need 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, 21, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 14, 14, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 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, 47, 48, 49, 50]) total number of confs: 104 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/977 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/977' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Cl)cc2Cl)CCCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458629459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458629459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001458629459 none O=C(NCC1(c2ccc(Cl)cc2Cl)CCCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens need 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, 22, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 14, 14, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 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, 47, 48, 49, 50]) total number of confs: 119 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458629459 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459 Building ZINC001458629459 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458629459 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 976) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCC1(c2ccc(Cl)cc2Cl)CCCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458629459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458629459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001458629459 none O=C(NCC1(c2ccc(Cl)cc2Cl)CCCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens need 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, 21, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 14, 14, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 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, 47, 48, 49, 50]) total number of confs: 104 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 977) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCC1(c2ccc(Cl)cc2Cl)CCCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458629459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458629459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001458629459 none O=C(NCC1(c2ccc(Cl)cc2Cl)CCCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens need 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, 22, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 14, 14, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 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, 47, 48, 49, 50]) total number of confs: 119 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458629459 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458629459 Building ZINC001458651948 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458651948 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/978 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1sc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C(=O)c2ccc(C)cc2)c1C) `ZINC001458651948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458651948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458651948 none Cc1sc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C(=O)c2ccc(C)cc2)c1C NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 1, 1, 5, 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, 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, 7] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 13, 13, 8, 13, 13, 8, 13, 13, 19, 19, 20, 20, 20, 20, 20, 20, 13, 13, 13, 13, 13, 4, 8, 13, 13, 8, 13, 13, 8, 20, 20, 20, 20, 20, 20, 20, 13, 13, 13] 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/979 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/979' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1sc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C(=O)c2ccc(C)cc2)c1C) `ZINC001458651948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458651948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458651948 none Cc1sc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C(=O)c2ccc(C)cc2)c1C NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 1, 1, 5, 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, 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, 7] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 13, 13, 8, 13, 13, 8, 12, 12, 19, 19, 21, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12, 4, 8, 13, 13, 8, 13, 13, 8, 21, 21, 21, 21, 21, 21, 21, 12, 12, 12] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458651948 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948 Building ZINC001458651948 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458651948 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 978) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1sc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C(=O)c2ccc(C)cc2)c1C) `ZINC001458651948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458651948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458651948 none Cc1sc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C(=O)c2ccc(C)cc2)c1C NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 1, 1, 5, 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, 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, 7] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 13, 13, 8, 13, 13, 8, 13, 13, 19, 19, 20, 20, 20, 20, 20, 20, 13, 13, 13, 13, 13, 4, 8, 13, 13, 8, 13, 13, 8, 20, 20, 20, 20, 20, 20, 20, 13, 13, 13] 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 979) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1sc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C(=O)c2ccc(C)cc2)c1C) `ZINC001458651948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458651948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001458651948 none Cc1sc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C(=O)c2ccc(C)cc2)c1C NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 1, 1, 5, 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, 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, 7] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 13, 13, 8, 13, 13, 8, 12, 12, 19, 19, 21, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12, 4, 8, 13, 13, 8, 13, 13, 8, 21, 21, 21, 21, 21, 21, 21, 12, 12, 12] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458651948 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458651948 Building ZINC001458692557 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458692557 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/980 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc2cc(Br)ccc2[nH]1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458692557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458692557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001458692557 none O=C(NCc1cc2cc(Br)ccc2[nH]1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 6, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 4, 7, 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: [4, 1, 4, 4, 18, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 18, 18, 43, 43, 43, 43, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/981 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/981' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc2cc(Br)ccc2[nH]1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458692557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458692557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001458692557 none O=C(NCc1cc2cc(Br)ccc2[nH]1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 6, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 4, 7, 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: [4, 1, 4, 4, 18, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 18, 18, 42, 42, 42, 42, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458692557 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557 Building ZINC001458692557 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458692557 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 980) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1cc2cc(Br)ccc2[nH]1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458692557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458692557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001458692557 none O=C(NCc1cc2cc(Br)ccc2[nH]1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 6, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 4, 7, 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: [4, 1, 4, 4, 18, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 18, 18, 43, 43, 43, 43, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 981) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NCc1cc2cc(Br)ccc2[nH]1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001458692557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458692557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001458692557 none O=C(NCc1cc2cc(Br)ccc2[nH]1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 6, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 4, 7, 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: [4, 1, 4, 4, 18, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 18, 18, 42, 42, 42, 42, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458692557 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458692557 Building ZINC001458771860 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458771860 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/982 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)c1ccc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c1) `ZINC001458771860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458771860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001458771860 none CC(C)(C)OC(=O)c1ccc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', '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, 1, 11, 1, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 50, 50, 35, 8, 35, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 3, 3, 3, 3, 3, 8] 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/983 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/983' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)c1ccc(Br)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c1) `ZINC001458771860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458771860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001458771860 none CC(C)(C)OC(=O)c1ccc(Br)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', '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, 1, 11, 1, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 9, 35, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 3, 3, 3, 3, 3, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458771860 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860 Building ZINC001458771860 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458771860 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 982) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)OC(=O)c1ccc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c1) `ZINC001458771860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458771860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001458771860 none CC(C)(C)OC(=O)c1ccc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', '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, 1, 11, 1, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 50, 50, 35, 8, 35, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 3, 3, 3, 3, 3, 8] 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 983) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC(C)(C)OC(=O)c1ccc(Br)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c1) `ZINC001458771860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458771860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001458771860 none CC(C)(C)OC(=O)c1ccc(Br)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', '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, 1, 11, 1, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 9, 35, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 3, 3, 3, 3, 3, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458771860 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458771860 Building ZINC001458866881 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458866881 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/984 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(C)(C)C) `ZINC001458866881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458866881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001458866881 none CS[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'S.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 6, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 17, 17, 3, 17, 17, 17, 17, 17, 17, 3, 3, 9, 9, 9, 9, 11, 11, 11, 6, 6, 2, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9] 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, 54, 55]) total number of confs: 82 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/985 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/985' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(C)(C)C) `ZINC001458866881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458866881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001458866881 none CS[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'S.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 10, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 20, 20, 4, 20, 20, 20, 20, 20, 20, 4, 4, 11, 11, 11, 11, 12, 12, 12, 10, 10, 2, 4, 4, 4, 20, 20, 7, 20, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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, 54, 55]) total number of confs: 97 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458866881 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881 Building ZINC001458866881 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458866881 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 984) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CS[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(C)(C)C) `ZINC001458866881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458866881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001458866881 none CS[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'S.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 6, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 17, 17, 3, 17, 17, 17, 17, 17, 17, 3, 3, 9, 9, 9, 9, 11, 11, 11, 6, 6, 2, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9] 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, 54, 55]) total number of confs: 82 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 985) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CS[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(C)(C)C) `ZINC001458866881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458866881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001458866881 none CS[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'S.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 10, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 20, 20, 4, 20, 20, 20, 20, 20, 20, 4, 4, 11, 11, 11, 11, 12, 12, 12, 10, 10, 2, 4, 4, 4, 20, 20, 7, 20, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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, 54, 55]) total number of confs: 97 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458866881 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866881 Building ZINC001458866884 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458866884 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/986 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(C)(C)C) `ZINC001458866884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458866884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001458866884 none CS[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'S.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 19, 19, 4, 19, 19, 19, 19, 19, 19, 4, 4, 10, 10, 10, 10, 11, 11, 11, 9, 9, 2, 4, 4, 4, 19, 19, 4, 19, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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, 54, 55]) total number of confs: 86 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/987 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/987' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(C)(C)C) `ZINC001458866884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458866884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001458866884 none CS[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'S.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 6, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 17, 17, 3, 17, 17, 17, 17, 17, 17, 3, 3, 9, 9, 9, 9, 11, 11, 11, 6, 6, 2, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9] 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, 54, 55]) total number of confs: 82 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458866884 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884 Building ZINC001458866884 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458866884 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 986) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CS[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(C)(C)C) `ZINC001458866884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458866884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001458866884 none CS[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'S.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 19, 19, 4, 19, 19, 19, 19, 19, 19, 4, 4, 10, 10, 10, 10, 11, 11, 11, 9, 9, 2, 4, 4, 4, 19, 19, 4, 19, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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, 54, 55]) total number of confs: 86 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 987) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CS[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(C)(C)C) `ZINC001458866884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458866884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001458866884 none CS[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'S.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 6, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 17, 17, 3, 17, 17, 17, 17, 17, 17, 3, 3, 9, 9, 9, 9, 11, 11, 11, 6, 6, 2, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9] 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, 54, 55]) total number of confs: 82 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458866884 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458866884 Building ZINC001458887282 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458887282 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/988 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2ccc(C(F)(F)F)cc2)CCCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458887282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458887282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458887282 none O=C(NC1(c2ccc(C(F)(F)F)cc2)CCCC1)[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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 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, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens 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, 11, 16, 24, 24, 16, 19, 24, 24, 24, 24, 24, 16, 16, 16, 16, 1, 1, 1, 10, 10, 10, 10, 13, 13, 10, 13, 13, 10, 4, 24, 24, 24, 24, 16, 16, 16, 16, 16, 16, 16, 16, 10, 13, 13, 13, 13, 13, 10] 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]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/989 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/989' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2ccc(C(F)(F)F)cc2)CCCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458887282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458887282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458887282 none O=C(NC1(c2ccc(C(F)(F)F)cc2)CCCC1)[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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 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, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens 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, 9, 15, 21, 21, 15, 17, 21, 21, 21, 21, 21, 15, 15, 15, 15, 1, 1, 1, 10, 10, 10, 10, 13, 13, 10, 13, 13, 10, 4, 21, 21, 21, 21, 15, 15, 15, 15, 15, 15, 15, 15, 10, 13, 13, 10, 13, 13, 10] 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]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458887282 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282 Building ZINC001458887282 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458887282 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 988) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NC1(c2ccc(C(F)(F)F)cc2)CCCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458887282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458887282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458887282 none O=C(NC1(c2ccc(C(F)(F)F)cc2)CCCC1)[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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 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, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens 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, 11, 16, 24, 24, 16, 19, 24, 24, 24, 24, 24, 16, 16, 16, 16, 1, 1, 1, 10, 10, 10, 10, 13, 13, 10, 13, 13, 10, 4, 24, 24, 24, 24, 16, 16, 16, 16, 16, 16, 16, 16, 10, 13, 13, 13, 13, 13, 10] 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]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 989) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(NC1(c2ccc(C(F)(F)F)cc2)CCCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458887282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458887282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458887282 none O=C(NC1(c2ccc(C(F)(F)F)cc2)CCCC1)[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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 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, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens 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, 9, 15, 21, 21, 15, 17, 21, 21, 21, 21, 21, 15, 15, 15, 15, 1, 1, 1, 10, 10, 10, 10, 13, 13, 10, 13, 13, 10, 4, 21, 21, 21, 21, 15, 15, 15, 15, 15, 15, 15, 15, 10, 13, 13, 10, 13, 13, 10] 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]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458887282 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458887282 Building ZINC001458929976 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458929976 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/990 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc([C@@H]2CCCc3ccccc32)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001458929976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458929976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001458929976 none O=C(Nc1nnc([C@@H]2CCCc3ccccc32)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 5, 5, 5, 9, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 5, 1, 1, 1, 6, 6, 6, 6, 6, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/991 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/991' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc([C@@H]2CCCc3ccccc32)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001458929976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458929976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001458929976 none O=C(Nc1nnc([C@@H]2CCCc3ccccc32)s1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 4, 1, 1, 1, 7, 7, 7, 7, 7, 2, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 7, 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458929976 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976 Building ZINC001458929976 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458929976 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 990) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1nnc([C@@H]2CCCc3ccccc32)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001458929976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458929976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001458929976 none O=C(Nc1nnc([C@@H]2CCCc3ccccc32)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 5, 5, 5, 9, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 5, 1, 1, 1, 6, 6, 6, 6, 6, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 991) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1nnc([C@@H]2CCCc3ccccc32)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001458929976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458929976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001458929976 none O=C(Nc1nnc([C@@H]2CCCc3ccccc32)s1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 4, 1, 1, 1, 7, 7, 7, 7, 7, 2, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 7, 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458929976 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929976 Building ZINC001458929987 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458929987 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/992 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc([C@H]2CCCc3ccccc32)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001458929987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458929987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001458929987 none O=C(Nc1nnc([C@H]2CCCc3ccccc32)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 8, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 1, 1, 1, 7, 7, 7, 7, 7, 2, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 7, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/993 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/993' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc([C@H]2CCCc3ccccc32)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001458929987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458929987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001458929987 none O=C(Nc1nnc([C@H]2CCCc3ccccc32)s1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 5, 5, 5, 9, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 5, 1, 1, 1, 6, 6, 6, 6, 6, 3, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458929987 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987 Building ZINC001458929987 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458929987 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 992) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1nnc([C@H]2CCCc3ccccc32)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001458929987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458929987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001458929987 none O=C(Nc1nnc([C@H]2CCCc3ccccc32)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 8, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 1, 1, 1, 7, 7, 7, 7, 7, 2, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 7, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 993) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: O=C(Nc1nnc([C@H]2CCCc3ccccc32)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001458929987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458929987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001458929987 none O=C(Nc1nnc([C@H]2CCCc3ccccc32)s1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens need 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, 5, 5, 5, 9, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 5, 1, 1, 1, 6, 6, 6, 6, 6, 3, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458929987 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458929987 Building ZINC001458948339 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458948339 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/994 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccc(Cl)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1C) `ZINC001458948339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458948339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458948339 none Cc1nn(c2ccc(Cl)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 27, 9, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 27, 27, 27, 27, 9, 9, 9, 22, 22, 22] 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: 60 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/995 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/995' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccc(Cl)cc2)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1C) `ZINC001458948339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458948339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458948339 none Cc1nn(c2ccc(Cl)cc2)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 27, 9, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 27, 27, 27, 27, 9, 9, 9, 22, 22, 22] 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: 60 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458948339 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339 Building ZINC001458948339 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458948339 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 994) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccc(Cl)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1C) `ZINC001458948339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458948339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458948339 none Cc1nn(c2ccc(Cl)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 27, 9, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 27, 27, 27, 27, 9, 9, 9, 22, 22, 22] 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: 60 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 995) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: Cc1nn(c2ccc(Cl)cc2)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1C) `ZINC001458948339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458948339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001458948339 none Cc1nn(c2ccc(Cl)cc2)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 27, 9, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 27, 27, 27, 27, 9, 9, 9, 22, 22, 22] 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: 60 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458948339 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458948339 Building ZINC001458952931 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458952931 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/996 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cnn1c1ccc(C(F)(F)F)cc1) `ZINC001458952931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458952931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458952931 none CCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cnn1c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', '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.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 17, 17, 9, 16, 17, 17, 17, 17, 17, 16, 16, 16, 16, 16, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 17, 17, 17, 17] 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]) total number of confs: 124 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/997 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cnn1c1ccc(C(F)(F)F)cc1) `ZINC001458952931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458952931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458952931 none CCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cnn1c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', '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.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 17, 17, 16, 16, 17, 17, 17, 17, 17, 16, 16, 16, 16, 16, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 17, 17, 17, 17] 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]) total number of confs: 91 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458952931 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931 Building ZINC001458952931 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458952931 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 996) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cnn1c1ccc(C(F)(F)F)cc1) `ZINC001458952931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458952931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458952931 none CCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cnn1c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', '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.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 17, 17, 9, 16, 17, 17, 17, 17, 17, 16, 16, 16, 16, 16, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 17, 17, 17, 17] 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]) total number of confs: 124 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 997) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cnn1c1ccc(C(F)(F)F)cc1) `ZINC001458952931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458952931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458952931 none CCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cnn1c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', '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.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 17, 17, 16, 16, 17, 17, 17, 17, 17, 16, 16, 16, 16, 16, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 17, 17, 17, 17] 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]) total number of confs: 91 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458952931 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458952931 Building ZINC001458965275 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458965275 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/998 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Oc1ccc(Cl)c(Cl)c1) `ZINC001458965275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458965275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458965275 none CC[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Oc1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 16, 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, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 7, 12, 3, 2, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 21, 37, 37, 35, 37, 37, 37, 37, 13, 13, 13, 13, 13, 7, 7, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 37, 37, 37] 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]) total number of confs: 117 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/999 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/999' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Oc1ccc(Cl)c(Cl)c1) `ZINC001458965275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458965275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458965275 none CC[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Oc1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 16, 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, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 7, 11, 3, 2, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 19, 36, 36, 34, 36, 36, 36, 36, 12, 12, 12, 12, 12, 7, 7, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 36, 36, 36] 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]) total number of confs: 117 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458965275 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275 Building ZINC001458965275 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458965275 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 998) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Oc1ccc(Cl)c(Cl)c1) `ZINC001458965275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458965275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458965275 none CC[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Oc1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 16, 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, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 7, 12, 3, 2, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 21, 37, 37, 35, 37, 37, 37, 37, 13, 13, 13, 13, 13, 7, 7, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 37, 37, 37] 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]) total number of confs: 117 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 mkdir: created directory `1' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275/1 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 1 (index: 999) grep: /scratch/xiaobo/182395/xbh-8058088.34/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: CC[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Oc1ccc(Cl)c(Cl)c1) `ZINC001458965275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458965275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458965275 none CC[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Oc1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 16, 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, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 7, 11, 3, 2, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 19, 36, 36, 34, 36, 36, 36, 36, 12, 12, 12, 12, 12, 7, 7, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 36, 36, 36] 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]) total number of confs: 117 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458965275 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 1: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275/1.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965275 Building ZINC001458965277 mkdir: created directory `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965277' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965277 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001458965277 mkdir: created directory `0' /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965277/0 /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965277 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/182395/xbh-8058088.34/working/3D/1000 `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Oc1ccc(Cl)c(Cl)c1) `ZINC001458965277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458965277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001458965277 none CC[C@H](CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)Oc1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 16, 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, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 7, 11, 3, 2, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 19, 36, 36, 35, 36, 36, 36, 36, 12, 12, 12, 12, 12, 7, 7, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 36, 36, 36] 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]) total number of confs: 112 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965277 /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Finished preparing ZINC001458965277 Recording results /scratch/xiaobo/182395/xbh-8058088.34/working /scratch/xiaobo/182395/xbh-8058088.34 Appending to /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.* 0: /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965277/0.* Removing working files in /scratch/xiaobo/182395/xbh-8058088.34/working/building/ZINC001458965277 /scratch/xiaobo/182395/xbh-8058088.34 Compressing combined databse files /scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/182395/xbh-8058088.34/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/182395/xbh-8058088.34/working/3D/1001' removed directory: `/scratch/xiaobo/182395/xbh-8058088.34/working/3D' rmdir: removing directory, `/scratch/xiaobo/182395/xbh-8058088.34/working/building' rmdir: removing directory, `/scratch/xiaobo/182395/xbh-8058088.34/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/logs `/scratch/xiaobo/182395/xbh-8058088.34' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbh' `/scratch/xiaobo/182395/xbh-8058088.34/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbh/finished' `/scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbh/finished/xbh.db2.gz' removed `/scratch/xiaobo/182395/xbh-8058088.34/finished/xbh.db2.gz' removed directory: `/scratch/xiaobo/182395/xbh-8058088.34/finished' removed directory: `/scratch/xiaobo/182395/xbh-8058088.34'